Tools->Options->Control Panel sets the default file type created when you create a new PCF and possibly the type used for Save Configuration As... dialog as well.

But, I bet 960 PCFs won't happily load into the 950. I'd be surprised but I bet you get a warning.

The versioning of the PCF is put in place such that prior to downloading the software can check against the remote type to know about possible compatibility issues. Versioning also allows the simulator to configure itself based on remote type. This is critical in the case of the 7000 vs the 7500 where there is a 16MB memory difference between the 2 remotes.