Hi Friend,
I just replicated your setup. I don't see any issues . still PEF-VPN license is enabled in both the controllers.
here PEF-VPN is controller specific therefore the redundancy or centralised license should not effect the PEF-VPN and VIA failover too.
May i know what AOS you are using ?
For your ref :

License status in Master :


License status in Standby :

Hope you got some more clarity on this :)
Please feel free to come back for any further help on this.