Hmm, i thought he might have meant you should be able to send your units to the HQ, and then use them to defend other allymates; which would be a horrifically abuseable feature.
And if you send units to the HQ, then as you say, there have to be downsides. The whole 'waiting for them to return' is a vital part of the whole combat system, if you could just auto return them i feel like it'd be abused. Also, not that i like to use the real life analogies, but since you started with them: if you send out a combat unit it takes awhile for them to travel to their destination, then they fight, and it takes awhile for them to return. We have not yet managed to create teleportation devices.
I think HQ Units are flawed, but mostly by their lack of imagination and minimal use; not because the mechanism is broken. Although there are several flaws with HQ units related to mechanisms, being lack of Eff/Bounty/Insurance (not sure about that last one but iirc you don't get insurance from HQ unit kills).