So Geany is currently GTK3, right? I am honestly asking, because I'm not sure if the Debian version 1.31 is compiled with GTK2 or GTK3, least of all how it looks like in other distributions.

You can find out in Help->Debug Messages it should say which GTK+ on the second line. Geany uses GTK+ 2 by default, but distros/users are free to configure it with --enable-gtk3. They both work OK, just the GTK+ 3 build gives all the ridiculous tablet-UI dialogs that plague GTK+ 3.

Even better, all settings of Geany, hidden or not, shall be represented in such an editable file without any GUI, or if needed, something like the "about:config" of Firefox.

That was the purpose of the Preferences->Various tab, though I think it may still be missing some preferences.

At last, it is indeed the same font it seems, hmm cannot complain on that one..

I've noticed on many occasions where Scintilla renders differently than native GTK+. The easiest way to see it is to use the View->Change Font dialog and compare what's in Scintilla (after pressing the Apply button) and what's in the little preview inside the font dialog.

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