I erased the two brace-lines from gedit.conf. Then I saved the document. I restarted Geany. When the zoom is 0%, then indeed I can't see brace highlighting. But in some zoom sizes (for example three times less than the maximum zoom) I can definitively see sometimes a change of the closing curly brackets and also the closing box brackets when moving with the arrow-keys. With other brackets, like for example round brackets or or angle brackets or the opening curly bracket, I don't see a change when changing the zoom size. So, my experience stands in contradiction to your statement:
... and although brace highlighting still happens the highlight is indistinguishable from the unhighlighted version.