Carrying a complete copy of Scintilla would bloat the repository size and might get relevant over time. Do you know and tried the already existing update script (https://github.com/geany/geany/blob/master/scripts/update-scintilla.sh)? It also just works on an extract tarball and copies relevant files and patches our changes in.
I don't argue against the git-subtree solution, it sounds pretty good actually. I'm just concerned about the repository size and duplicating efforts which have already been done in the above mentioned script.