Three issues, though one could definitely be me. When I try to put a rally point on a starbase, I get one above it. You're saying that I should be able to do that?
Second issue is what do you do once you're done building that starbase? Is there a way to move a rally point? If so, I can't find it, if not, I'd need it to use it this way. Without that, I have to destroy the old rally point, create a new one, and then go and tell every planet to use the new rally point. Major pain.
Last issue, and not a very important one, is the micromanagement of sending just a few constructors each to several different starbases when I get a new upgrade is a pain.
So, on that subject, while having some kind of "constructor govenor" would be nice, being able to move rally points would make up for most of the problem, as long as any ships in route to that rally point immediately change course rather than waiting until they get to the old rally point and then update their autopilot. (or maybe make that an option, so you could say "enough constructors are heading that way, all new constructors head this way").
Yet another possible solution would be a "rally point govenor" that could change all ships with rally point A as their destination to rally point B, or change all planets with rally point A as their rally point to rally point B. Being able to see how many of what ship types are bound to each rally point would also be nice, as I could say "That's enough constructors for that starbase" before actually finishing the starbase.
While the constructor govenor sounds like a nifty idea and better for the problem of constructor micromanaging, I think either of the other two ideas are a bigger win overall, since they can also apply to military rally points. I'd also guess either of the other two ideas would be considerably less effort. They do nothing for the third issue which is very minor, but do address the second issue, and the first issue is probably somewhere between my neurons and my mouse.
Not married to any of these suggestions, but I would like to see one of them in the game to reduce micromanagement.