Ukraine was part of the Soviet Union, that is true. But the Soviet Union was ethically very mixed and united many peoples under one roof. I think certain areas could therefore be well treated like seperated "occupied" countries. I don't know the exact effect of Ukranian freedom/resistance fighters neither on the Wehrmacht nor on the Red Army. I just took this example to show that there can still be resistance groups in countries even if there is a) no government in exile (GiE) and b) that are completely occupied (like I said, we can count Ukraine as being occupied, since the resistance movement came from within and was not supported by Moscow, at least not the independence fighters afaik). Maybe the example was not perfect, I give you that.
In the game Ukraine is part of the Soviet Union in 1936, owned and controlled by them with cores. There is no country of Ukraine.
In 1941(ish) in the game Germany invades Ukraine, there is still no country of Ukraine. Germany doesn't own it and doesn't have any cores. It occupies this part of the Soviet Union. And there are partisans.
There is no GiE, because there is no country of Ukraine, and therefore no government to go into exile. The government is that of the Soviet Union. They are not a GiE. They may (as real life) still be located at Moscow, or the capital may have moved to another city.
The partisans in the game are abstracted to be supported by the Soviet government not by some non-existent Ukraine GiE.
You say that the resistance came from within IRL. This is not correct. Many of the partisans behind enemy lines were originally Soviet Red Army members. As the German blitzkrieg advanced 100,000s of Soviet troops were surrounded in pockets. But significant numbers escaped, and continued operations behind the lines. Plus local Communist Party activists from the occupied areas joined.
While originally suspicious of these groups that were no longer under direct Red Army command, Stalin was persuaded to support them. Arms and supplies were provided by the Soviet Union. And further members were parachuted behind German lines. By the end of 1941 some 90,000 men were operating in partisan detachments across the occupied area (Ukraine, Poland, Byelorussia and a few in the Baltic States). The numbers grew from local recruitment, and from mid-1942 there was central organisation of operations by STAVKA (Soviet High Command).
Full details of these can be found here:
https://en.m.wikipedia.org/wiki/Soviet_partisans
These were joined by some groups which were independent of the Soviet operations. Some nationalist groups of men who had survived the civil war existed, or were formed from younger men, who did not want to return to Soviet control of their homelands. But appear to have been small in number and less effective, without the military support that the Soviet partisans got. And because the Soviet partisans were not above attacking them, or providing intelligence to the Germans about them.
There were also groups like the Bielski Brothers (Jews who escaped from the Polish ghettos) who were accepted by the Soviet partisans. The 2009 film "Defiance" was based on their story. It's worth watching.
Once the Soviet Army recaptured areas, partisan detachments generally disbanded. But in some cases they moved ahead of the front line, deliberately remaining in German occupied zones to continue to cause maximum disruption to their logistics.
I'm not aware of any Ukrainian nationalist groups fighting on once Ukraine was returned to Soviet control. I'm not saying there wasn't any, but they were probably short-lived and had no significant effect, because they had no external support. After the effects of German occupation, the Soviet Army was generally seen as a "liberating" force. The lesser of two evils.
The game makes no acknowledgement of internal forces like this anyway. Your example of the IRA for instance (who didn't operate in mainland UK until the 1970s) is not relevant. Internal opposition is only abstracted, and appears in the game if the level of support for their ideology reaches levels to force government change or civil war.
In the game, Soviet forces recapturing Ukraine returns full rights to the Soviet government to the manpower, factories and resources of the region. And also when they re-occupy Eastern Poland.
But that is not the case if Soviet forces advance into Romania, Hungary, Western Poland etc. Then they are the foreign occupiers and are subject to partisan activity, until the Axis surrenders and they can "liberate" the countries under communist governments or puppet regimes.