Upgrading Apps in ROMs

[Guest gorf1000]

I was toying with the thought of cooking a ROM because I'd like to have a ROM that includes PointUI Home2 (and I'd like to challenge myself with the task). I'm curious though, since Apps that are included in the ROM (at least the official ones) cannot be uninstalled, can they be upgraded? I'd hate to have to rebuild the ROM every time there's an update. With that thread as well, part of using Home2 is customizing it with themes and applets which need to be placed in the program's main folder. Is that hidden when it's built within a ROM?