While true, there can certainly be a trade off. As it is, the player already gets the luxury of not having to worry about colony ship cap, and defense in depth shall shift to becoming even more powerful then it already is. Not having to micro rebuilding is a very powerful benefit...
This optional micro reduction should help manage a large empire; it shouldn't be nearly as efficient as microing a colony ship unless you can adapt the AI to deal with this.
We are getting into a subject here which has a very long past, which may be necroed - fair warning....
Your thinking of this as a game element, when it's meant to be an interface convenience for the player. It doesn't allow you do to anything new, but it makes things a little easier on the mind of the player. Personally, the "changing gears" of planning an offense only to be interrupted by rebuilding a command station is the worst part - it's not about the time needed, it's about the interruption and distraction from more fun elements.
Also, I'd be happy if there was no delay on the rebuilding as well. I only suggested it hoping to appease X and Keith (they are friends of the AI).
Well, I consider it a game element. If you could automatically rebuild, you inheriently gain more time to do other things. For me, during mid to end game, theree is often 2 or 3 minute minute delay, on average, between clearing out a planet and dragging the colony ship to rebuild, unless I'm are first starting out or microing everything. To rebuild instantly is simply abusable, and actually not really practical (if even possible) using other methods. The closest you can get to simulate that is to use MK III engineers and to bring in colony ships via teleporting shuttle, which costs quite a bit a knowledge. So the player DOES gain an advantage, because they can rebuild their planets their economies faster, defenses, etc. faster.
But the AI reaction is what I am more concerned about. If you can quickly automatically rebuild the station after the AI has been cleared, then any future ai that pass through the world will take a swipe at that station. When you have the ability to do this over many worlds you have an automated delay mechanism for the AI that does not involve caps. Given enough time, I am confident I could find a way to exploit this to making the AI take at least 5 minutes longer to hit my homeworld from any direction by distracting them. Those 5 minutes can change a game during an exo or CPA.
You really need at least a 3 minute delay to keep it as an automated, back up rebuilding.