Ahh. Right. That is slightly more of a tangle. 
Are they showing these custom fields on signup? If so, I think they’d need to keep the custom field for Location as I’m not sure you can have the default one on the signup form (same for if they’ve included the extra columns in the user directory too).
(That’s more to do with which you’d consider to be the ‘primary’ one, rather than being able to dispense with either)
I think you may be left with copying the custom field value to the default location. 
(and hiding it to make it more ‘meta’ data just for the Location plugin to use)
Could this be an addition to the Location plugin to cater for this for everyone?