The Custom RTC widget is under the influence of the computers System Locale.
The format strings are not necessarily related. As a small example, setting the Windows Language to Dansk, and then trying to use yuzu in English the requested AM/PM indicator is simply not shown
The display format for the Custom RTC field needs to be removed from src/yuzu/configuration/configure_system.ui
modifying the display format needs to be moved to src/yuzu/configuration/configure_system.cpp