War of the Roses is unfortunately a topic I'm not as well versed in as I should be. I can, however, comment on The Hundred Years War which is fairly close chronologically.

Rape was certainly widespread in the Hundred Years War and was definitely seen as a problem. Armies, both French and English, wrought significant devastation on the areas they marched through both in the food they took and in the violent acts they committed. However, most of the time it was also widely condemned and periodically various commanders made a concentrated effort to prevent, although pretty much always with mixed success.

The French were obviously always encouraged to try and stop rape and plundering on the part of their soldiers. The King of France was obviously not supposed to be ransacking lands he technically ruled. The French Church, including the Avignon Papacy, was particularly keen to see this kind of thing stopped.

The English in contrast were pretty happy to sow destruction and discord for much of the war. While rape was not an explicit element of the Chevauchee tactic it certainly happened on those raids quit a bit. However, during the later reign of Henry V when it looked like he really could take the French crown he did a pretty abrupt about face on the issue. The Future King of France could hardly be seen to endorse violence against his rightful subjects and so Henry began efforts to limit the violence his own armies committed. Disobedient soldiers could be summarily executed for their behavior and while this doesn't seem to have stopped rape it seems to have limited it.

One thing you see a lot of in GoT (or at least the two books of it I read) that I haven't come across much in history is nobles raping people. While there is certainly an element of our sources probably white washing the behavior of their subjects it's worth remembering that the code of Chivalry was pretty explicit on how women were to be treated and there would have been a lot of social pressure to not violate that. Some nobles also brought their wives on campaign, which would be a further reason not to go about raping women. In a similar way, noble women were often (although not always) spared the fate of rape that peasant women would have suffered.

David Green's The Hundred Years War: A People's History has some great information on this. There's also a chapter on noncombatants in Medieval Warfare which was edited by Maurice Keen. I can't remember the author of that particular chapter right now though.

I'm unsure whether this is acceptable for this subreddit, but I just wrote an article on this very topic (I'm a medievalist myself). It deals primarily with the question of the commonality of marital rape and the cultural acceptability of rape (and I link to a number of books and articles on the topic there): http://www.publicmedievalist.com/got-rape-and-middle-ages/

I can't speak to the very specific time period that you discuss (with apologies). But the TL;DR of that article and my understanding was that, first off, marital rape was not considered to be rape (no matter who was raping whom). Rape outside of marriage was considered a crime but prosecuted far less often than you might think, and with some rather odd exceptions (marriage by abduction, etc.).

As for warfare, I'll reproduce a comment I wrote about it earlier when someone else asked a similar question (found here: https://www.reddit.com/r/AskHistorians/comments/14gpkl/was_medieval_war_full_of_raping_and_plundering/):

Rape in medieval warfare seems to have been fairly common, though there was some conflict about it. Rape was generally condemned as wrong, and doing against the commands of your superiors could result in punishment. And there were some commanders who took measures to prevent it. Take for example one Thomas, a commander of the English at the assault of Canes (1346), who rode through the streets and prevented the rape of a number of women by his soldiers. The fact that he had to do this implies that it was somewhat endemic, and the fact that it bears mention implies that his preventative measures were uncommon.

Source: Saunders, Corinne J. Rape and Ravishment in the Literature of Medieval England. Woodbridge: D. S. Brewer, 2001, p. 141.

There were other examples where rape by soldiers was condemned, not just by superiors but by peers. Take for example the story of Thrakesion, a Varangian (meaning, a Norseman hired into the elite guard of the Byzantine empire). Thrakesion raped a woman, who afterwards took his sword and killed him. His compatriots, discovering this, gave the woman all the man's effects and buried him in an unmarked grave.

Source: Laiou, Angeliki E. Consent and Coercion to Sex and Marriage in Ancient and Medieval Societies. Washington, D.C.: Dumbarton Oaks, 1998, p. 167.

However, this begs bigger questions-- like 'to what degree was this behaviour endemic' or 'how much of this would have been going on after any given battle'? The sources are necessarily limited, and it is possible that some bias has crept in-- were rapes mentioned in chronicles as a way of further villifying a enemy? Or were they not mentioned consistently since they were so par for the course as to not be worthy of mention?

It's a question of interpretation and, I believe, empathetic historical imagination. Most soldiers during the Middle Ages were conscripted footmen or aristocratic groups of sargeants, squires, knights, lords and so on, with a minority being professional mercenaries. Whether an individual in one of these groups might be inclined to rape someone post-conquest requires a consideration of the culture, their peers, their individual psychology and the psychology of rape. It's a very complex issue and one which I don't think anyone can answer perfectly, but I think it's important to mention that there would have been people-- probably many-- in each of those groups who would find widespread rape, even after conquest and when tacitly allowed, abhorrent. Thinking otherwise requires us to imagine medieval people as fundamentally different to ourselves, lacking in empathy and any kind of compassion-- subhuman beasts and criminals. This plays into the pervasive myth that medieval people are lesser than we are-- more violent, less 'advanced', even (perhaps only slightly, but still...) sub-human. And with a topic as charged as rape, it's difficult not to think in these terms.

So, to sum up, was rape pervasive in medieval warfare? Probably, with some exceptions. Does that mean that every medieval soldier was a rapist, or found it morally acceptable? Certainly not. How would modern people behave in the same situation? Well... that's a difficult question now, isn't it?