Comparing GTK2 and GTK3 was not your initial issue.

Possibilities:

GTK2 and GTK3 do not render the same, quite likely, they are different and likely have different versions of Pango and harfbuzz the two libraries that actually convert font info to pixels.
The fonts are not the same, or not the same version with the same hints
The Scintilla rendering has changed in the versions between Geany for GTK2 (limited to Scintilla 3.5) and current git GTK3 (Scintilla 5.3.7)

As we don't have access to your system you will have to do the research, 1. and 2. you will need to check dependency versions for the libraries mentioned and versions of the fonts.

To see if there have been any changes in Scintilla operation you can check its changelog on its website.

Quite frankly the GTK3 looks right, having aliasing only on one side of the verticals as the GTK2 shows is "unusual".

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