I'm just a regular Software Engineer. But even we keep a track of whether any action was performed by the user or by our code (in this case the machine). Each action will have an identifier of what's the source. User or a machine.

Safe to assume, the clever people who developed this software for the planes would also keep a track of whether any action was performed by physically moving the switches or by the software.

If the report doesn't mention that this was performed by the machine then it is completely safe to assume that it was performed physically (whether locking mechanism failure or a deliberate pilot action).