Well I just had this thought, maybe when you pause an upgrade on your commander the "upgrade animation" should be stopped as well, at least because it technically isn't upgrading anymore.
Appart from "realistic" considerations, it could become a small tactical option : for example by pausing the commander upgrade when you see a scout approching, you make your commander look idle to enemy and therefore avoid being rushed at once because they know you can't move, overcharge, etc. It could also prevent enemy scout from discovering if you are upgrading gun or T2, and thus avoid that they react accordingly.