I think you can compare them to some extent, especially when it comes to drive-by downloads, which are exploit based attacks. As of now, both programs seem to be able to defend you very well, but there is not enough information on how MBAE exactly works to compare it with Sandboxie in detail.
Sandboxie will probably be a bit stronger when it comes to protecting the system, because it treats programs under its supervision generally like they have already been compromised. On the other hand I suppose MBAE can stop attacks that don't require breaking out of an restricted environment and establishing persistence.
For example, I think Sandboxie wouldn't have protected you against something like the FBI exploit for the Tor browser, because in that case start/run- and internet access restrictions / closed IPC paths / stopping code injection into other processes wouldn't have helped, as it was all happening inside the browser process.
Personally, I really like both of them.