"It is likely that different versions of CQL will need to be created for different FHIR versions, as the same information could be in a different resource. The app will have access to the FHIR endpoint, it should check the version and then retrieve the package that has been created for the correct FHIR version."

This statement has no relevance.  DTR is constrained to FHIR 4.0.1.  If and when a future version of DTR actually supports other versions of FHIR (a long way off), it can address how multiple versions should be handled (where US Core hasn't already done so).  Right now, there's no guidance we can or should give.