Running a few more tests and comparing the working and non working systems it finally turns out the issue is related to the ZFS kernel module. The working Bookworm system is a standard netinstall using default settings (single boot partition) where as TrueNAS has multiple ZFS partitions. So they are not the same but got me one step further checking deeper on ZFS compatibility. I came across the following forum posts:
ZFS 2.2.0 Released: ID mapping of unprivileged containers during mount
Migrating LXD 5.20 → Incus 0.5 on Ubuntu 22.04 LTS (ZFS 2.1.5) and shiftfs support?
Which was pointing me in the right direction to update the zfs module on the non working system. TrueNAS was released with version 2.2.3-1 which should contain full id-mapping support but doesn’t obviously work with incus (properly because of TrueNAS modifications). So I followed the instructions from @stgraber at ZFS builds which installed 2.2.4, rebooted and the permissions denied issue was gone.
Success, now I have a working TrueNAS with Incus LTS which is pretty cool!
Leaves one obvious question what is the difference between @stgraber zfs sources compared the TrueNAS tree? ID mapping is still a new feature in zfs and as such it will take some more time for stabilisation? May be @stgraber can give some useful input which area to concentrate on to find the needle in the haystack.