I would agree with your suggestion to just manually upgrading from Scintilla 3 to Scintilla 5 first, without any changes to process.
Don't even worry about changing the upgrade scripts and stuff to do that major upgrade, its only happening once, just get the first Scintilla 5 Geany working manually, then modify/create scripts to suit a process of small upgrades, hopefully huge upgrades like this will be rare (pending Neil adopting C++20 :open_mouth: )
I am not sure if I will be personally much help, having never done a Scintilla upgrade either, but will try time permitting, and hopefully more experienced heads will chime in.