Some precisions: May be can you add an USE flag for --with-gtk=2.0|3.0 option. And an other for python USE flag already registered in vte-0.28.1-r200.ebuild. I think that should be better for the next version. Reproducible: Always
No. With a USE=gtk3 use-flag, you can't install only the gtk3 library — you'll always end up installing the gtk2 library as well. Both slots are parallel installable, and there is no need for a 'python' use-flag with the gtk3 version since you're supposed to use it through gobject-introspection. There's nothing to do here.
I had didn't think about that... Sorry. In all cases, the version for gtk2 no longer exists in the next version.