Custom fonts are still used with the switch off
An easy place to reproduce it is in the reader mode, see the title. Here I set the font to a nonsense one. When custom fonts are enabled, it's used throughout the reader mode, but even if it's disabled, it's still used in the title.
It also happens on some webpages, so it's not just reader mode. I would expect it to never ever be used if custom fonts are disabled.