Generally speaking, most any backcountry water source in the USA will not be much of a risk for viral contamination, so your decision to omit the viral filter and only filter for bacteria, parasites and cysts ought to be entirely safe.

I don't have experience with the system you are asking about, but the major reason for bumping up to a 4-liter system would be if you expect to have a fairly large hiking party needing water. The 4 liter system might be more convenient in that case, even if it is heavier.

Presumably, you would be able to pour off filtered water into other containers/bladders/bottles out of your 2 liter system and then refill it.

BTW, I use a gravity filter these days and do not miss pumping at all.