Just like medieval Europe, the Mongol rulers had a somewhat flexible attitudes towards concubinage, inheritance, and illegitimacy. But while there are some important points of similarity and even contact--yes, Mongol khans married illegitimate Byzantine princesses--the mix of politics and sexuality played out in a specifically Mongol fashion.

First, let's talk about royal women's responsibilities. Pawns though they might be in their families' use of marriage to form alliances, Mongol queens generally did not have the chance to be ornamental. The most important responsibility was running the various camps that the particular nomadic group lived in. Just like Mongol rulers had multiple wives and concubines, there would be multiple camps; just like there was a senior wife whose children had inheritance primacy, there was a senior camp.

This is actually where we get to see a little female solidarity and community, actually. The wife in charge of a camp was generally also in charge of the other wives and concubines living in it. While their sexual common denominator got bounced around from camp to camp, leaving the groups of women separate most of the time, periodically they all got together for festivals and ceremonies.

That could even be a rare bright spot for women whose marriage to Chinggis (or later rulers) was the result of the devastation and surrender of their people and slaughter of their family. Tatar princesses Yisüi and Yisügen survived the utter destruction of the royal house in 1202 to wind up as junior brides of Chinggis, who ended up running different camps but still met together. The daughters of the conquered Kereit leadership did not have husbands quite so prestigious...but they brought with them their servants, retainers, younger brothers, and a strong social and informational network.

(ETA) I should point out that above, I am talking specifically about high-status women of conquered peoples--royal women generally becoming wives, lower-ranking ones becoming concubines. However, as mentioned in a follow-up comment, medieval warfare across the tri-continental world was synonymous with victorious soldiers raping, enslaving, and/or murdering the people whose cities and villages they stormed. We have basically no firsthand accounts of surviving rape, or even women talking about surviving rape in the abstract, from the Middle Ages in general, much less from Mongol women--Christine de Pizan in 15th century France refers to rape as "the greatest sorrow", and there are enough traces of 'tragic backstory' sermon illustrations to show that yes, surviving rape could have a devastating long-term impact on women's lives. As far as their children went, though--remember, the medieval world had no DNA tests, and was strongly suspicious of women's sexual mores as a baseline. "Legitimacy" was as much a matter of recognition and acceptance as genetics.

Royal women, particularly those in charge of camps, controlled their own economic resources, including horses. They received a cut of tax revenues and of war booty, even! They could also be active in politics, especially but not only as widows. Töregene, for example, fought long and hard to keep the throne secure for her son. In other cases, women took on an intercessory, informal diplomatic or "peace-weaving" role. Elite women also could and did actually attend formal political assemblies, including as advisors.

It's important to recognize that not all royal women controlled their own camps. This was a question of seniority among wives, but also other factors institutional and not--social rank of their birth family, nature of the political alliance or conquest that brought them to Chinggis and the other men of his family, straight-up favoritism. The subordination of some queens to other women could be a major blow to women who had commanded significant power among their birth family and people, as they were now largely excluded from political roles.

Queens and royal concubines thus definitely had a limited sphere of action overall in heavily sexist and patriarchal Mongol society. However, they could push at boundaries and wield not just power but legal authority in their own right. And it was based at least partially on their own elite descent rather than just who their husband happened to be.

With senior wives, junior wives, concubines, kidnapping brides from conquered peoples, exchanging brides and grooms among allies, and different wives holding power over their own camps, Mongols had a roomier definition of marriage than we might expect. As shown above, this is reflected in the commonalities among royal women's lives independent of how they came to be Chinggis' partners or their place in that hierarchy.

But that hierarchy did matter, and not just in terms of who got to run the richest camp. The senior wife was the most important, and the royal succession descended through her.

In some cases, that had the result you might expect. Chinggis paid a lot more attention to having children with his senior wife, Börte, than he did with his other wives, even after she either hit menopause or said, "Nope, sorry, this uterus is closed for business." (...It's still the Middle Ages, so more likely the former.)

On the other hand, in practice the situation was fuzzier. One of his wives was probably pretty stunned to find he had traded her, like property, to one of his allies. One son of Chinggis, additionally, actually altered the hierarchy among his wives to make a different one senior and thus the "real" queen mother.

With an established principle of succession and a hazy idea of the "sanctity of marriage," all the other royal children were on somewhat more equal social footing. In other words, without regal inheritance on the line, there was less of a need to draw boundaries around legitimate and illegitimate children. In fact, sometimes it was outright impossible. How these children fared was up to the present situation, needs, and desires of the parents (as in Europe, women could be very active in calculating marriage alliances for their children). There wasn't really a parallel to the western European practice of "oh, sorry son, you can't hold the throne but have a nice cushy bishopric", but junior sons could inherit property and participate fully in the politics of marriage.

~

I want to stress that scholars are juuuust starting to take seriously the study of Mongol women and especially queens. (Jack Weatherford was ahead of the game!) Bruno de Nicola, Women in Mongol Iran: The Khātūns, 1206–1335 was published in 2017 and Anne Broadbridge, Women and the Making of the Mongol Empire just this summer. What I've related above will surely be questioned, expanded, altered, and reinterpreted in coming years. As a Latin medievalist, I especially can't wait until scholars with the linguistic chops start working on Europe-Near East-Mongol comparative queenship. But it's an excellent start.

I have a somewhat related question based on a misconception I often see during discussions on this subject, including in OP’s question. Discussions about this phenomenon often talk about how 17,000,000 people are descended directly from Genghis Khan, whereas the original paper (Zerjal et al. 2003) explicitly makes the prediction that the Y chromosome lineage arose several generations before Genghis, and was shared by his male-line relatives (i.e. any brothers, sons of his father’s brothers, etc.).

Given that, how many of those descendants are likely to be of Genghis himself vs. his male-line relatives? Biologically it seems likely that it would be a smaller proportion, but I don’t know what other social factors might have played into that, or how many male-line relatives might have been around at the time.

Question: How the hell do we even know this? We still don’t know where Genghis was buried so how can we trace his genome to millions of people?

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I thought it was just a theory that Genghis Khan had this many descendents. I remember hearing about it on radio lab. Has something come out recently where one can claim this as fact now?

Sorry to piggyback off this post, but what exactly are illegitimate children and are they any different (from a paternal side) genetically from those legitimate children?