The passenger standing by for F with a confirmed F ticket has priority over any upgrades for the empty seat. I'm not sure what the agent sees these days but in the past the agent had to check a separate queue. I was once at the top of the upgrade list but did not get the one open F seat because there was someone with an F ticket standing by. But I know of plenty of other examples where the agents are fixated on complimentary upgrades from Y and ignore the F standbys. Whether it's out of ignorance of the rules or laziness, the effect is the same.

Of course, if you have a coach ticket and are standing by for the flight you must be cleared onto the flight in Y, after upgrades of confirmed pax. If there are still empty F seats after that then you can get the upgrade.