I don't know if this was the case in Brawl, but footstools appear to have their own special buffering property that makes a Jump command cause you to footstool an opponent if they get in range up to 10 frames after you initially pressed Jump. This is completely unaffected by whether or not you have your mid-air jump(s) or whether or not you're pressing it during the cooldown of any other air command you can buffer another move after (this basically just means you can't buffer a footstool out of a Ledge Jump) You can't footstool anyone until the IASA frame of the current command, of course. It also doesn't seem to have a "fail" window and doesn't care if you're already holding a Jump command when you press Jump.
tl;dr--If your character is capable of footstooling someone within 10 frames of pressing Jump, you will do it, and as soon as possible. If you press a Jump command every 10 frames or faster, anyone that gets in range of your potential footstool will be footstooled on the frame they get in range as long as you keep pressing Jump repeatedly.
This could be a big deal for punishing people who consistently airdodge under the ledge before sweetspotting Up-B, since even if some airdodges only have two frames of vulnerability, this will catch it as long as you're in range during those frames. Apparently, airdodges are among the "unfootstoolable" commands, so if the opponent buffers via Attack or Special afterward, they can't be footstooled.
Still, since Ledge Jumps don't allow people to buffer commands out of them, this makes footstools a fine choice for punishing Ledge Jumps as characters with momentum-shifting moves. For example, Ganondorf can Down-B immediately afterward. This actually makes for a great way to cover multiple ledge options, as footstool -> Down-B beats Ledge Jump, and the low double-jump that happens when you're not in range lets you avoid Ledge Attack and punish both Ledge Attack and Ledge Climb (and, likely, a ledge hopped aerial for a spike KO!) if you're timing it to hit a Ledge Climb.
EDIT: boop