OK, the MSR MapCruncher team has contacted me with some clarification as to the difference between the versions and what that means for the future:

You are correct that one reason there are two versions is licensing. The other reason is branding and support: the VE team has quality standards and wants to ensure they don’t find themselves doing support for a buggy product. We in MSR, on the other hand, are more interested in shipping bleeding-edge tools, even if it means things break. Right now, there’s not much in the MSR branch that’s not in the VE branch (other than a few undocumented hacks). But we’ve got some really exciting stuff in the pipe, and having that MSR branch available means we can turn out experimental versions very quickly. Then, if it gets a positive reception, VE can decide to push it through the product-quality process.

Well there you go. Currently MSR MapCruncher is at version 3.2.4 and VE MapCruncher is at 3.2.0. We’ll see how things change when MSR MapCruncher makes a bigger jump ahead. But at least for now VE MapCruncher has a license that allows you to use it in a commercial setting so I suspect most would be better served with the more stable version.