I don't know. Someone told me "it may even be more secure than the wrs's" or something very close to that. Molebox first compresses your files. Next, it encrypts them into a 128-bit encryption key. The main difference between standard and pro (supposedly for Molebox and not Gamestudio), is that standard cannot pack DLL's, one major reason why I don't like the 6.4x update - the engine is now a DLL instead (I wished it was still an EXE though). With standard, you won't easily be able to update your program (such as program updates or patches for bugs you've fixed).
I'm not able to compare WRS's because I can't use them (can't afford pro edition and my spending limit forbids it entirely). The comparisons will not be accurate as a result.
Compression - Molebox supports it, but I don't know about WRS's.
Encryption - WRS's are supposedly encrypted, but don't know for sure. Molebox uses 128-bit encryption.
Multiple data packages (multiple related files) - Molebox Pro supports it (not standard), but I have no idea with the WRS's and how they are.
Application integrity checks - not exactly sure what this does, but it supposedly checks to see if the program is actually in working order.
This comparison chart helps explain a few things. It seems like Moleboxed EXE's are just as secure (or even more secure) than WRS's, but I have a baseless estimate, the second-least accurate kind of estimate. Because I can't make WRS's, I can only guess.