How to build a Modification package for app using modern settings?

I strongly agree that this is a show-stopper. PSF launch scripts would be eventually handy, but the problem is they are tied to an entry point via an application entry, and modification packages sadly do not override nor add applications... Even if the original app already uses PSF, its config.json is not in VFS path, which means that overriding the original setup is not possible. Other solutions (like overriding executable entry point with a custom wrapper that ensures the data is initialized in a proper way) are way too "hacky", and also work only if the app installs itself to VFS. And re-packaging the original app with a new identity just to bring the required settings kills the update chain and the whole idea of separation of apps from their add-ons/modifications.