And it may help on the destack problem.
Personally, I do not see a huge problem with the stacking issues. Not saying I dont see them, I just dont let them annoy me enough to ruin my games. However something like you suggest wouldnt hurt and would also help that historical aspect.
My suggestion, if a region has Formal Alliance with a Parent region, then the only agreements it should have with the colonies are Air and Sea Transit treaties and Non-Aggresion Pacts. If its possible to implement that way, it wouldnt allow any foreign units into a colony other than aircraft and navies along the coasts. It also may help the stacking problem if its involving foreign units in colonial ports and piers. The problem I think , is that a Formal Alliance is hard coded to included all those transit treaties plus the LOS and Non-Aggresion and Colonies are probally hard coded to have Formal Alliances with the parent. If its not so, I dont why Fistalis or another modder hasnt modded yet.
Either your suggestion or my suggestion though, IMHO, requires an additional treaty which gives another region authorization to help defend that colony (and only that particular colony) on behalf of the parent. It should very hard to acquire permamently and easy to acquire for say six months to a year. Longer than that the difficulty getting it should go up.