MFA can be enabled for Dynamics 365 at a service level where it is enabled either for all environment/instances or none. There is no option available to enable MFA for specific D365/CDS instance / Environment.

In a situation where most of D365/CDS based application/instances do not require MFA, it becomes challenging to onboard a sensitive application in same tenant that requires MFA for compliance/regulatory requirements.

Regards,
Kunal Murarka