When you say that there is no way to tell the nativization to look for other files, there does seem to be a way to guide it to find missing header files:
"Fixing Missing Headers
Many projects have an “aggregate” header: either [GameName]/[GameName].h, or [GameName]/Public/[GameName].h.
If you add the path of this header to FilesToIncludeInModuleHeader, under [BlueprintNativizationSettings] in DefaultEditor.ini, you can fix many issues related to missing headers."
This is from Blueprints Visual Scripting in Unreal Engine | Unreal Engine 5.2 Documentation
So I was thinking maybe there is a way to make it look for other files?