@ralf3u thank you for the detailed reproducer.
I do not see any change in the characters themselves, but what there is is a change in the background.
This is as instructed by the gedit theme (with the edits as above) because the `current_line` sets background to `#edeceb` but when the cursor gets to the the brace, the background is set by the `brace_good/brace_bad` to `#fff`, I'm not sure thats `#ffffff` or `#f0f0f0` :-S but its different to `#edeceb`.
So as I said in the first place, it can't be turned off, and have to add now that all the visual changes can't always be hidden, although they can be minimised, since the background of the line at the caret brace is `current_line` until the caret is beside the brace and if the other brace is on another line the background will be the `default` value, so one of them will change since the brace settings cannot have two values. Maybe you can minimise it by setting the brace backgrounds to in between.
As I said I don't see changes to the character, but with the characters enlarged that much, maybe what you are seeing is a change in anti-aliasing (which is blending the character colour with the background colour, which changes). That has had changes between the Scintilla in Geany 1.38 and 2.0. Or maybe there is something different in the versions stack of rendering software I listed above between your system and mine.