As Rmr25 said, it's not difficult to fold and roll the tent so the weather doesn't get at the inner, any more than it does when putting up the tent at the end of the day. I collapse the tent flat, outer on top, fold the tent longways, outer to outer, with the groundsheet exposed, then roll.
If the inner does get wet, it will be from condensation on the inside of the outer. If there's much, I devote a few minutes to wiping it off before taking the tent down (wipe and wring, usually with a J-cloth that lives in the peg bag).