Ever since the LJ release that redesigned the default pages, I'm using custom comment pages myself, just because Arial as a font is not very eye-friendly for me. So, I definitely don't have a problem with others using custom comment pages as well, but if it's something like a dark gray background with light gray font in a font size that's like 6pt, I really get the urge to backclick immediately. But then I remember that there's style=mine, so I add that to the url and that obviously solves the problem. If the text is hard-coded, though, and remains unreadable even with style=mine, I won't bother with the fic.

I even add style=mine when someone's using the new LJ default comment page, just because I prefer my own layout. So, as long as you don't hard-code your fic, it really doesn't matter to me which option you're going with. If I were you, I wouldn't even bother with turning off custom comment pages if that's what you're using and comfortable with.