According to this documentation https://docs.microsoft.com/da-dk/fslogix/configure-office-container-tutorial - UPD and and FSlogix Office containers only works in include mode. We have testet this in our testinvironment and this is unfortunately correct.
We need to use the exclude mode because of other apps that will not run in include mode. The date of the announcement in the above link is November 2018. Is there any updates regarding getting UPD and FSLogix Office containers working in exclude mode?