I don't use a pack liner, but when I did, the only thing I felt I HAD to keep in it was my quilt, my camp clothes if appropriate (down jacket, generally) and sleep clothes/change of clothes. Dirty and wet gear went either in the pack but on top of the close liner and either in its own stuff sack or just packed on top, or it went in one of the outside mesh pockets (especially shelter). I didn't care it the shelter got wetter (though all of my shelters are cuben so they don't 'hold' water and get heavier, inner nets went inside the pack).
I think, unless you're in a downpour for hours on end, most packs will keep most water out, for the most part (lots of mosts in that sentence!), so wet items packed inside the pack but outside of the pack liner won't get wetter (wring them out as much as possible, of course, before packing them). There's always stuff you don't care about getting wet, and these things can go outside in the mesh, or outside of the liner but in the pack as well.