Question regarding skin customization document

edit

I want a deeper customization for my website using Askbot and according to the document,

Deeper customization by editing default skin

Since the default skin still will change (a major redesign is expected), the best method for deeper customization is via use git revision control on a clone of the askbot master repository. It does require some knowledge of git system.

Some questions:

1. Is it okay modifying 3rd party app even though it is just the templates and skin?
2. Is it better to modify only templates but create a separate skin directory which consists only of media folder but not templates?
3. If am doing this way, is it better to use Zurb foundation instead of Bootstrap since Askbot is going to be moved to Zurb anyway?