When assigning an "Audio Conferencing", "Phone System" or "Calling Plan" license to a user via PowerShell, while the Skype for Business app in the major license is disabled, the licenses will not be provisioned. In fact the license will be marked as "Disabled" when querying the license service status via PowerShell.

(Get-MsolUser –UserPrincipalName user@domain.com).Licenses.ServiceStatus
MCOPSTN5 Disabled
MCOEV Disabled
MCOMEETADV Disabled

This means a user currently requires an enabled Skype for Business app in his major license (e.g. E3) to use Audio Conferencing or PSTN Calling in Teams. When the SfB app is disabled after the license provisioning is done, there is no issue. Hence I think this dependency is a bug that could potentially be resolved quite fast.