When creating a new VI Workload Domain and choosing to specify license keys, the bundled OEM license key is automatically used for vCenter. There is no option to specify the purchased license. So deployment always uses the OEM key for the vCenter.
license.log
YYYY-MM-DDT16:17:49.034Z invocation-vmomi-executor-3 operationID=61583128 WARN server.core.oldmanagement.impl.LicenseAssignmentManagerImpl Missing license key AAAAA-XXXXX-XXXXX-XXXXX-BBBBB. Adding it back to inventory
YYYY-MM-DDT16:17:49.050Z invocation-vmomi-executor-3 operationID=61583128 INFO server.core.oldmanagement.vmomi.LicenseAssignmentManagerMoImpl updateAssignedLicense result:LicenseInfo AAAAA-XXXXX-XXXXX-XXXXX-BBBBB
SDDC 5.2.x
This is by design.
Choose "License Later" when creating the Workload domain and specify the license afterward manually.