I think even without false flag operations it would be difficult to keep Baltics within the USSR for long, from what I know they were the only ones where significant part of the population hated USSR and never accepted it.
I don't think so. There was and still is a significant Russian speaking portion of the population in the Baltics, and a lot of support for the Bolsheviks during the Russian Revolution came from the Baltics. The extreme anti-Soviet attitudes you would have encountered in the 80s were not as prevalent earlier on. The problem is that the anti-Soviet propaganda, first by the Nazis and later by the West, started much earlier in the Baltics. The largely autonomous governments of the Baltic republics were very lax in combating western infiltration and nationalist subversion, while Moscow never paid much attention, or, in the case of the treasonous Gorbachev clique, deliberately ignored the problem. This was a general problem that went further than just the Baltics, in that insufficient attention was paid across the USSR to ideological education and establishing a Soviet national identity. The problem of the Baltics is that just like western Ukraine they were exposed to the brunt of western infiltration and agitation during the cold war, along with having a history of Nazi collaboration.
Yes and yes, but not by communists, unless and until there is a real demand for it from a significant portion of the population. It's a question of strategic timing. If communists push for something for which the conditions do not yet exist, it would be counter-productive. Communists have to devote their time and effort to that which is most likely to advance the cause, and right now that is not separatism (except in occupied Hawaii and Puerto Rico).