The internal borders of the USSR fall into two different categories: those that largely existed prior to the USSR/joining the USSR (so the South Caucasus states, the Baltics, arguably Ukraine); and those created within the USSR (Central Asia is the main example here), with some exceptions. I'll try and answer the specific examples you cited here, and then give a more broad overview answer:

• Nagorno-Karabakh - While mainly populated by ethnic Armenians (then, and now), Karabakh is not easily accessible to Armenia, especially in 1920 when the Bolsheviks occupied the region. There is currently just one road connecting the two, a highway through the mountains that was only properly built in the 1990s and funded largely by the Armenian Diaspora (and is the reason Armenia occupies part of Azerbaijani territory not within the former Nagorno-Karabakh Autonomous Oblast, which was separated from Armenia by a strip of territory). In the 1920s there was no such road, and it was incredibly difficult to travel between NK and Armenia; however there are no mountains blocking the path to the rest of Azerbaijan, and the main road leading up to Russia (via Georgia) is to the east as well, and indeed is how the Bolsheviks first came to the region (they occupied Azerbaijan first). There was discussion on joining Armenia and NK together, but it was deemed impractical due to communications issues (see the road issue again), so they linked it to Azerbaijan, while making it autonomous. And until 1988 that largely worked.

• Central Asia - First it should be noted that both the five Central Asian states (Kazakhstan, Kyrgyzstan, Tajikistan, Turkmenistan, Uzbekistan) and the others you mentioned (Tatarstan, Buryatia, Chechnya) are all republics, though the first five were made full union republics, while the others were merely autonomous republics within the Russian Soviet Federative Socialist Republic, and still exist in the modern Russian Federation. Now obviously you mean why did Kazakhstan et al become union republics (and later sovereign states), but I wanted to make sure that was clear. It had to do in part with the policy of state-building in the USSR: they were reluctant to create union republics unless the state had international borders. In part it was to entice local ethnic groups on the other side of the border to join the Bolshevik cause and allow for a stronger future claim for expansion, what Terry Martin referred to as the "Piedmont Principle" (after the region in modern France that was the origin of the Italian unification movement). The autonomous states obviously couldn't serve that purpose, so largely were left as they were. There is more to that, but I'm blanking at the moment and would have to look into it, so please ask a follow-up if interested.

• Fergana Valley - This is something I can't actually answer, but I do know of a couple books that look at the Uzbek-Kyrgyz border, of which the Fergana Valley is part of. I'll mention them below.

• North and South Ossetia - Situated right between the two Ossetia's are the Caucasus mountains, making it extremely difficult to travel between the two. The Russians built a military highway in the 1800s to reach Georgia, going through modern South Ossetia, but even then it was treacherous. The easiest way to go between the two is the Roki Tunnel, which was only finished in 1984. Thus it was easier to just keep the two places separate, though some argue that it was also done in order to antagnise the Georgians, who had the South Ossetian Autonomous Oblast (or region/province) to contend with; I would dispute that argument, and agree it was a more practical consideration.

• Tajiks in Uzbekistan - I don't know what specific regions you are mentioning here, but it is worth considering that the modern ideas of ethnic Tajiks, Uzbeks, Turkmen, Kazakhs and Kyrgyz only dates back to the Soviet conquest of Central Asia. The people there largely did not identify as such, and the Soviets themselves largely created the ethnic identities based on a more rural-urban divide (with the Uzbeks being considered more urban). Thus it was considerably difficult to properly sort everyone into "their own" republic (yes, Tajik is a Persian language while Uzbek is Turkic, but even then Uzbek was only formalised in the 1920s, and Tajik was made distinct from Iranian Persian in that era; plus the people there were multi-lingual, so it was not easy to divide them that way either).

• Karakalpakstan - I unfortunately don't know the details behind that at all, so couldn't really tell you.

• Central Russian borders - Again, these people were only really identified and categorised in the early years of the Soviet era. While they had lived there for centuries (or more), they never identified as a specific group, and were largely named as one group or another by Soviet ethnographers. The borders for their territories were largely drawn to encompass their largest concentrations, though without ethnic cleansing that was near impossible (and the Soviets didn't do that in those regions; that type of thing began decades after the borders were drawn).

It is important to note that prior to the Soviet Union, many of the non-Russian peoples did not have a concept of a national identity as we understand it today. Many of them didn't even have a written language or literary tradition, which while not a definite factor in fostering a national identity, certainly helps it. The Soviets introduced these ideas to them, even though the very notion of nationalism was contrary to Marxist theory. However Lenin argued that these peoples were so backwards they needed to develop a national consciousness in order to advance to the point where they could move into the socialist phases. Thus the policy of korenizatsiia (коренизация; loosely translated it means "nativization") began, which Martin linked to affirmative action (non-Russian peoples were promoted to high government positions, given university spots, culture developed, etc). This also fed into the creation of national territories, which the Bolsheviks felt was important for their development (an idea not shared by other socialist groups at the time, but I digress). Ethnographers were sent out to figure out who lived in the Soviet Union, so they could be properly developed and advanced into the modern era, and then onto socialism. But of course no region is homogeneous, and thus things like the examples you mentioned happened.