From: east coast, usa
I can't answer your specific concerns, but can relate my experience as the Axis vs the Allied computer, with my Axis attacking Russia in 1940 [before the Soviets can occupy the Baltic States]. Lithuania and Latvia fall easily as they have only one small garrison unit. Estonia may be a little harder because of the distance to Kallinn and its' ability to be reinforced by the USSR. [Historically each of these countries had three or four divisions of mobilized infantry, so no match for either Germany or USSR].
Overall, this move makes supply better for the Axis as each of the Baltic States has better supply than if Soviet occupied. It is also easier to get thru them as you are only up against the one garrison unit each. I see only advantages to this if you are attacking Russia in 1940 [which is overall not the best move, but is an option]. It makes me think that if the Axis moves to occupy any of the three, then they should all be occupied by Russia. However, this could be difficult to script given various possibilities.
I have not seen any increase in USA mobilization when I [Axis] have attacked the Baltic States.
Also, you can reach Leningrad quicker, but your line becomes more extended as the advance thru the Minsk-Smolensk area is still slow. Therefore, you usually reach Leningrad with a minimum of units.