Also: If the input wave is at (eg.) 11024Hz you'll go in and out of phase with the ADC producing beat frequencies and all sorts of horrible artifacts.
Nope, you are thinking curve fitting, not filtering.
11024 in at 44.1K system will have (abscent reconstruction filters) a component present at 11024, and one at n * (44100 +- 11024) for all positive integer n, when you filter off all the higher components you get just the 11024 AT the level you started with irrespective of the sampling phase.
Consider that Fs/4 example (because the math is easy) 0,1,0,-1 Vs 0.707, 0.707,-0.707,-0.707, now both uniquely specify the same periodic band limited signal, as they must given that if there were any harmonics present they would fail to fit within the band limit (Second harmonic would be Fs/2 which fails to fit), so the only waveform that data can represent is a sine wave, which just leaves the question of amplitude.
Well, 0,1,0,-1 as a sine wave clearly has an RMS power of 1/Sqrt 2, as clearly does 0.707,0.707,-0.707,-0.707, so the amplitude of the only component that fits into the band limit is the same, irrespective of the sampling phase.
Regards, Dan.