Intersting thoughts.
Right now, it obviously doesn't seem like you can lock rally points to moving troops.
Once you do that, though, this would seem to suggest that ALL units will move to the army (like in starcraft 2).
I agree that this is PROBABLY a good way to deal with the issue... simply adopting the starcraft trope.
You basically produce to the rally point. Always.
Done. It could be that simple.
BUT...
I also like the idea that you can SEPARATE regular unit production from reinforcement production.
I like the idea that I can call reinforcements from my armies, and still be able to send troops elsewhere, without extra clicks.
I would therefore suggest that you should maybe be able to add a reinforcement rally point, which is separate from regular production rally point.
I don't want to over micro, and I often put all factories of a single type under a specific control key... but...
... yeah... tough issue.