As far as to "when" they removed Einstein... if they had removed him before the 1st Red Alert, then that means exactly what you said, the chrono tech and Prism Tech happened later.... in the ORIGINAL time line, but those technologies might have been developed earlier then, since they didn't have a viable WMD like nukes etc... because if you notice, the Allied weapons are based upon particle acceleration technology, i.e. the Proton weapon. Chrono tech is a variant of particle acceleration theory.
Like you said, it seems they may have in fact screwed up the timeline, b/c on the EA Forums
Link for RA3, the claim is that Hitler was wiped in 1924 in the RA1 and then Einstein was killed in 1927 by the Soviets, but if that's the case, that means he didn't go back to kill him, b/c Einstein was dead... if you want to get deeper, if Hitler was dead b/c of Einstein going back, then in the future... why would Einstein have built the time machine? To go back and kill someone that doesn't exist? You wouldn't remember that which did not happen...
It's also easy to conclude that the corporation known as "Futuretech" in the game, may have taken Einsteins work and continued it, i.e. Mirage Tech etc. and not nuclear weapons...
Captain Janeway on ST:Voyager said it best...
"Time travel. From my first day on the job as captain I promised myself I'd never let myself get caught up in one of these God-forsaken paradoxes. The future's the past, the past is the future. It all gives me a headache."As far as the Amphib warfare thing... I am quoting the EA development team... take it up with them.