Create/modify your unit plans in a PLN file (be it the same file as your building, or a separate file) -- MOD files are not meant for working in, they are more like "vessels" of information for import. Publish your unit plans to MOD (with the desired layers on/off) and hotlink those MOD files into your building model. For your enlarged unit plans, work in the original PLN. Layers will not be an issue. The only "disadvantage" to this method is that you have to publish to MOD prior to updating the hotlinks.
MacBook Pro Apple M2 Max, 96 GB of RAM
AC27 US (5003) on Mac OS Ventura 13.6.2
Started on AC4.0 in 91/92/93; full-time user since AC8.1 in 2004