I don't know what to think about this. The OP makes an excellent point but on the flip side of that, isn't there supposed to a huge tradeoff with federations? You get a whole new fleet with all the best techs from all federation members and you have complete control while president. The penalty is that when you aren't president, one of the other leaders has complete control and may take you in a direction you aren't interested in going. If you don't want to risk fighting wars that only benefit your allies, and run the risk of delaying your own expansion perhaps by decades, then just stay as allies, don't form a federation.
However this begs the question of how being allies with federation members woks. Take for example, in the Blorg stream, one of their allies asked to form the federation, I'm curious what would have happened if the Blorg said no. Would the federation have formed anyway, just without the Blorg? And if so, would the Blorg still have been allies with all of those empires? I guess the question is can a player empire be allies with an AI empire that is in a federation that the player does not want to join? Because I can see that causing some problems if you either have to join the federation or lose your allies. And if you can remain allies with empires in a federation but not join yourself, how does war work, can you call them in, can they call you in? The more I think about this the more questions I have.