Obsidian is already coded to interpret mod based on the operating system. It already changes what is expected. A fair choice at that. The issue is, without decoupling sync, the modifiers are coded as opposites. Managing modifiers across apps is complicated.
Mac’s command is also more synonymous with the windows key. In keyboard building they are both referred to as gui. It doesn’t make sense to swap mac’s command to where the ctrl key is due to all the fixed mac shortcuts associated with it.
An alternative would be platform specific hotkeys so obsidian can nest into a current workflow with minimal fuss. However, changing the interpretation of mod might be simpler.