[neatoman]

His relationship with the leadership role and Raph's claim to the role mostly seems to be a "Let's allow the guy who wants to be in charge think he's in charge" type deal. It's pretty obvious throughout that Leo really leads the team by planting ideas tricking people into doing his bidding, while allowing Raph to believe he's in charge because that's distracting to the enemy and because it satisfies Raph's ego.

It's not an arbitrary last minute thing Splinter just does to troll the viewer, in-universe he probably caught on to what Leo was doing all along and decided it was best to make it official.