As I understand Commander does 3 things:
* Mod manager similar to JSGME
* Basic career editor
* Career pretty print
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So, if you want its functionality, you will need to install at some point while creating SH3 build. Like JSGME, it changes files, but has an auto undo function. (achieved by acting as a launcher; see a Microsoft Process Manager and you will SH3.EXE running as a child of SHCTR.EXE). Thus, I think if you make the changes, turn off rollback, and launch once/exit ... you have probably patched SH3 with Commander ... I assume the patch is done at launch as it make most sense) This is why you are told to undo your Commander changes (if no rollback) before using JSGME. (I think this is probably why auto rollback was added.)
So, you can really bypass the SHCTR.EXE acting as a launcher. The only reason I can see to do so is to use a custom command line or not inherit system properties from SH3 Commander. (It worked for me fine.)
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Finally, be aware that there are quite a few customized SH3 Commanders for GWX, NYGM, Vanilla, ONEALEX, etc... Basically, they use different CFG files that result in alter mechanics and pseudo randomness like variable crush depth or a thermocline layer. YOU NEED TO GET THE RIGHT COMMANDER FOR YOUR MEGA MODE.
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I hope that helps.
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