This issue has been declared normal function.
It kind of makes sense but also does not make sense. When selecting how a parameter is to be controlled, a snapshot should not effect other types of controlled parameters (ie. a snapshot should not change a parameter set to be controlled by a Midi CC#). Other parameters that are not controlled do not change but then again they are not changed between snapshots.
I added a request for Snapshot bypass for Parameters here:
https://line6.ideascale.com/c/idea/1049072
Kind of like Snapshot bypass on blocks but for individual parameters.