actually your paradox is sort of not a paradox: a mysterious time traveler killed Hitler in 1924, and in 1928 some other man killed Einstein. They are part of the same timeline, obviously if grandfather paradox was in effect in the time-travel mechanics of Red Alert, there would be no point for Einstein to go back in time once he eliminated Hitler (the past stays changed once changed).
However I have to agree Allied chronosphere is weird (though I guess Futuretech invented it), and that goes tenfold for Tanya's "time belt" (chronotravel. is. lethal. for. humans!!!).
Drones can't swim (that would be silly), nor can they fly, or paralyze tanks.
I don't see why Japan would be in a constant conquering battle, but if ineed they are as powerful as you think, WTH was wrong with all the intelligence in the world?! I know Cherdenko and Kukov are from a parallel time line, but didn't spies in this timeline notice a massive buildup of forces near the far eastern border?
For that matter what happened to the real Cherdenko and Kukov? The ones from this unverse?
I'm not even going to ask how killing Einstein made Japan into a superpower. It's the one free pass they get.
However If Einstein is out of the picture, why didn't Alternative-Alternative-Wold-War-two succeed (the one with this universe's version of Stalin)?
Finally, and this pales in comparison with my above complaints, Einstein didn't invent the Atomic Bomb, I found references to an explosive that uses sub atomic energy in Glossop's "The Orphan of Space" from 1926, you might find earlier references. Indeed Einsein's letter was not specifically meant to encourage FDR to build The Bomb, but rather to warn him that the Germans were making one. You can bet diamonds to toothpicks that by 1972 (the year of Red Alert 2's WWIII, and the earliest year the opening sequence of RA3 could be happening) the atomic bomb would be invented. Plus the soviets have a G-d D---d Atomic reactor!