No, it won't make much difference. We are currently providing pthreads wrappers in Wine, and we'll need to do basically the same thing for NPTL. So if the current wrappers don't work for Mono the new ones probably won't do much better; we need to find a proper fix for that problem regardless of the underlying thread implementation.
But what is the fix? IIRC the basic problem was the Wine internal pthreads implementation conflicting with the one linked in via libmono and libgc, something like that.
Is this the "ELF symbols have global scope" problem come to bite us on the ass yet again, or does it go deeper than that?