It's rare that people will upgrade a lot of radars, but it's normal to upgrade multiple support factories and mexes.
It's only fair to make people pay extra for the privilege of upgrading a shield in place when a certain faction can't even do that at all.
It just comes down to this: do we want to give people the option to do a little song and dance, to trade APM in exchange for about 600 extra mass? Or do we want to streamline the game here.
I'm definitely in favor of streamlining the game by equalizing the cost of upgrading in place vs. ctrl-k trick. The game is complicated enough. Making it a little simpler here is more good than bad.