I have been able to resolve the permission problems and so all folders are synced now. Solution for permission problem is here.
The only issue that is left is performance, but I am not sure if the shown transfer speeds are correct because if they are, how could I have transferred like 700 gb in just a few days?
On the network side, I understand that ipsec isn’t ideal, but the sophos sg backend doesn’t support wireguard. I guess I could install a wireguard client on the truenas, but I am not sure if that will be faster or not.
I am open to suggestions!