Yes, the higher the value of the cap, the more treble the tone control will roll off. So with the .022 the sound will get less dark (with the tone on 0) than with the .047.
I think it'll be fine - I like quite a dark tone, especially from the neck pickup, and .022 works fine for me. On newer guitars .022 is pretty much the "industry standard" nowadays anyway, even with single-coils.