The engine is not made to pass orders to arbitrary units. It only works for units that are currently in your selection. We'd need to hack in suggestions (1) and (2) through construction.lua and that is a file that is, uuhh - not friendly towards developers. The fact that it (the file) even works at this point is a miracle.
Child factories for carriers already pass the units they create back to the parent, so there's some linking between them?
This is in the sim, where the external factory unit passes the events to the main unit. That triggers the animations and effects and cleans them up again.
I assume that with (3) you want the factory unit to become unselectable. If that is so, then you'd also remove the ability to set rally points.