It doesn't sound right, though, that a fix for this should
involve the user having to mess around with intiialisation
order etc. -- it should "just work".
It seems that this might be a worthwhile project for "someone"
to work on? (Perhaps they could fix the problem of not being
able to un-apply themes at the same time?)
I don't really understand what you suggest doing: the .emacs file is
read *after* creating the first frame, so there's no way to avoid
"flashing" without breaking some .emacs files.