It's OK to add fields to existing requests, this doesn't break backwards compatibility. In fact that's one of the reasons for the fixed request size.
and you can tell which fields are valid from the protocol version number I assume
another point: as of today, at startup, the link to wineserver isn't done when the protocol version doesn't match... so, it seems you'll be removing this test after the protocol freeze (or at least that the protocol version returned in init_thread is greater the frozen protocol version)
A+
PS: any answer on the reasons for not applying the toolhelp patch?