Agreed, but do you reckon its worth the effort to ask system programmers whether or not they'd be willing to accept UX contributions?

You can always ask, but many programmers aren't going to be able to/don't have the desire to communicate with non-programmers in useful ways.

I wrote about the problems open source projects often face getting design (and other non-technical) help they can use: http://opendesign.foundation/articles/import-designers/

Your article highlights some of the key issues faced in this context, by both developers and designers. Fauxflake seems to be a completely developer oriented project, so there would probably be a marginal benefit from UX applied to it (of course docs and tutorials would make a difference). I think projects like Audacity that are meant to be used by the layman, probably stand to gain the highest with better design.