Hi, and thanks for your work so far. :)
When this ticket was created, we didn't have the list of enabled mods included in the commands.txt file. Now that we have that, it should be possible to check that the list of enabled mods is the same as in the commands file.
Currently the check is done in the visual replay menu but not when using the command line. I think a mismatch in the mod lists should trigger a warning instead of an error, so people using the command line are still allowed to do what they want.
This would be a more complex task. Would you be up for it? You can come to our IRC channel if you need more information.
Also, for next time, please take a look at our new way of SubmittingPatches: we're making changes to our review process.