I don't think this problem is specific to CX bikes, especially since road bikes tend to have geometry and headtube angles as tight and steep or more so than CX bikes. Frankly I'm surprised you haven't had this problem before. From what I've read and what I've heard toe overlap generally only happens on smaller frames, like a 52- 54cm. It shouldn't be too bad just have to be a little more careful with the pedals on those tight turns.
I'd agree with Hamilton. I ride 50-52cm bikes depending on the geometry and I always have toe overlap. Geometries on news bikes are somewhat tighter than older frames due in part to a preference by pros for quicker steering over comfort.
the jamis is a pretty tight little bike - short wheelbase, chainstays, steep angles. that creates more overlap than some bikes. i believe the nova pro and supernova have the same geometry - so upgrading wouldn't help here. you could go slightly shorter crank, more rake, etc. but those are prob changes you don't want to make.
maybe try a fitting to see if you're set up well? maybe there are ways to move the cleat more forward and still take care of your knee?