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Commands added through commands.add_command in script.on_init are not available after save + load. This suggests that added commands do not persist between save + load. Since I can't find any documentation on it, this might be intended behaviour, and not a bug. If it is intended, please note that in the api doc. (Looking at that doc, I think either game_commands or commands should have a different description than the other. Their difference is currently not clear.)

Edit: I was informed that this is intended behaviour. So please see this bug report as a request to mention this in the api documentation.

I have no idea how this should work, so I'm leaving it on Rseding91.

That's intended behavior. Commands work identically to events in that you have to re-register them every time the game starts.

The docs are already changed in 0.16 to say so.