Congratulations  And good question.  

In a bed, their roots will spread.  And you’d definitely need to follow up on the transplant or likely experience unavoidable root loss if delayed by 2 or 3 years.  

Larger pots would keep them confined, but if not ‘large enough,’ they can become rootbound…   Also, pots need to be watered more often - And, 'dug in,' surrounded by insulating material or brought in during hard freezes; pots will freeze from all sides.  

I’ve watched both methods used, with the key to success being timely follow up.  Pots seem most popular… as they’re portable.  Seems many a fruit tree are growing ‘too close to something’ due to the fact, “That’s where I’d temporarily heeled it in ...and forgot about it!”  

Just don’t forget about them 

Yeah, I have some M26 apple rootstock in my raised bed vegetable garden that is pretty much taking over due to circumstances that Viron touches on.  

If I dig it up and transplant it this spring, I bet I'll still be getting root suckers for some time to come.  That's not the worst problem to have.