This seems to be a fairly common (mis?) conception among gate agents.
Normally, upgrades are processed before standbys, so by the time you clear standby there's not usually any available seat in F, making the question "are cleared standbys eligible for upgrades?" completely moot. But occasionally there are still empty seats in F by the time standbys have cleared.
Once you clear standby you should be treated just like any other pax on that flight. In other words, you are "on" that flight-- there's no going back as your seat on your original flight is released (I don't know how it works behind the scenes but this is definitely how it appears). GA should not be able to essentially treat you like a second class citizen because you were previously standing by. Like others, I have had successful and unsuccessful attempts at clearing an upgrade after clearing standby. The problem is that it's not automatic-- the GA has to add you to the list after you clea. Here is where it leads to the problem described by the OP, and where GAs apparently need some additional training...