You could make these exact same arguments for a regular battle, right? But the thing is, both are much more difficult. Boosting is harder because instead of queueing up against your alt and forfeiting to yourself to immediately gaining points, you actually have to win the game. Sure, in theory it's a 2v1v1, but that's not foolproof. Ghosting with a random stranger is also unlikely to be as effective as working with someone outside the battle independently that you know, unless you're imagining two players who know each other and happen to queue up together. But if two players decide to form a temporary alliance and discuss their plays together, that isn't ghosting - imo that's how part of how the format should work. Ghosting is receiving help from an individual outside of the battle, but there's nothing wrong with asking an opponent for help during the battle. It's a free-for-all; even if their alliance succeeds, suddenly it's a 1v1 and one player is bound to have the advantage. So an alliance may be terminated early in order to avoid losing in that 1v1, but doing so too early may be risky, etc.
In the FFAs I watched on YouTube back in the day, it was 4 people constantly making and breaking alliances, working together only to immediately turn around and attack the ally. I just don't see the problem with players who are opponents communicating with each other.
There might be an argument to make about blocking PMs between allies in a multi battle though. At serious Multi Battle side events at live VGC events, players can't communicate by speaking with their partner at all. But I've personally never liked that rule much, because restricting communication with your ally in a format where you're already working together is kind of awkward. For Showdown, it would also be trivial to avoid such a PM restriction by using a third-party platform to discuss their moves (presumably you couldn't do this in a FFA, as you wouldn't know the opponents beforehand).