Largely it's the time commitment. Next it's the amount of learning that can be harder on a novice dog and handler.
Small things can supposedly come into play too, such as back jumping is frowned upon in agility at a foundation level but the dog must immediately return over the jump in IPO, the Aframe is higher and I have heard it can interfere with their striding techniques plus it can confuse their contact process (from what has been warned to me), also for my boy it was a world rocker when I asked him to park it (heel position on the right) and while it's better he learns it we have run into some frustration of him trying to offer the wrong heeling during bitework to cheat nearer to the helper. My TD is convinced training B to turn left and right has encouraged his spinning which makes tie back bite building a headache but since he never spins in the blind I don't pay much attention to it. I did get talked to at his first trial because his default when confused is to go into a hold and bark on me and that's not exactly smiled upon at agility. Like I said, little things, no big deal for experienced handlers but they can be troublesome and added headaches.
Over all it's not a bad thing to be a jack of all trades but it appears to help the dog and handler to have a main focus until they've mastered it if they want to go far.
Of course here I am with two ipo/agility/akc obed dogs that started in flyball, compete in dock dogs, have dappled in lure coursing, nose work, and I'm considering trying my hand at Rally with Sloan this fall. That said I do believe Backup is a dog who'd benefit from a much narrower, stringent training schedule, however he's stuck with a dappler owner for now.