Changing text and some positioning, or the pre-sets for what modules are shown, seem like reasonable things for themes, to me. Changing the presentation options is dicier, but if it's just adding something, then that also seems quite reasonable. The theme style sheet function was implemented specifically so that themes could have more options than just colors, fonts, and images, after all.

I do think that, if a theme is sufficiently changed that it's not readily recognizable as a child of its parent layout, then the theme author should be encouraged to make it a new layout, but that's a case-by-case sort of thing. For general guidelines, I'd be very inclined toward "anything that's provided for within the S2 core is allowable".