(In reply to Miguel Angel Ajo from comment #2)
> It seems like NetworkManager is fiddling with the tap device, while it
> should not be doing that.
from the logfile it is not clear that NetworkManager actually touches the device. It certainly should not interfere, but the logging messages alone don't indicate that NetworkManager interferes.
If the problem is reproducible, please enable debug-logging of NetworkManager and provide the full logfile.
You do that, by configuring
[logging]
level=TRACE
in /etc/NetworkManager/NetworkManager.conf, followed by `systemctl restart NetworkManager`.