Custom DPI setting should not apply to GTK3+ apps, if GTK3 scaling is not 1.
GTK3+ has a design flaw. It uses own internal integer scaling multiplier for UI scaling, instead of DPI, unlike all other component libraries/widgetsets. So when you set scaling to 2x in Appearance - Settings, only GTK3+ apps are scaled. GTK2 and qt apps remain tiny. They rely on DPI. But when you change DPI in Appearance - Fonts, fonts (only) in GTK3+ become double scaled. Somehow MATE and Gnome do something about it, so DPI setting does not apply twice for fonts in GTK3+.