Personally I wouldn't worry about lots of clearance. "Tight" is just fine. Once one is riding, then one isn't standing on the top tube.

You don't necessarily want the seat slammed down on the Top Tube, but even that is acceptable for young kids.

So, if he can stand over a 56 without being uncomfortable, then get it. Or, snag a bike with a sloping top tube.

Make sure you have a little extra upward seat post adjustment.

I agree, go ahead and snag a good used bike. Kids can be hard on bikes, or get them stolen.

I'm partial to the older "classics", but it doesn't hurt to also target a cheaper bike from around year 2000. Probably aluminum frame.

Any plans of racing?

Oh, also, consider getting a bike that you can work on together. Perhaps build a set of new wheels from scratch. A few other "upgrades" to get him used to doing some bike maintenance.