As far as I remember there are two problems related to GTK versions:
- Having KiCad and wxPython build againt different toolkits results in
wxWidgets symbol conflicts when wxPython is loaded.
This issue should be resolved by linking KiCad against the same library
as is used for building wxPython.
- Rendering/printing problems in eeschema and pcbnew.
This one is already fixed by providing GAL renderer for eeschema and
pcbnew. As you have correctly noticed, legacy renderer is broken with
GTK3 in pcbnew and eeschema, so I think it is reasonable to disable it
there in the initial stage.