No, it wouldn't.
I mean, yes you could do it, but it wouldn't work very well.
I asked Paulages once about using stock 650 pistons and a 650 head in the bored 550 jugs and bottom end.
There was some small difficulty with that, can't remember what it was, but that's probably the direction I'd head.
The longer stroke isn't waht makes up for "larger combustion chamber". It's the shape of the piston dome. It isn't like you can shove the straight edges of a piston into the semi-spherical chamber by giving it a longer con rod. The shoulder of both the cb550 and cb650 is probably a milimeter or so below deck height. Any higher and the pistons would be kissing stuff they shouldn't be.
Sorry, went off on a tangent there. Long story short: No, your compression will be too low.