Hello! So I loaded up your config and tried it out, but I wasn't able to reproduce the issue - I attacked a base (as a PVP player) that was owned by a PVE player and I was not able to damage it.
However, I did notice something about your config - you have Chat notifications off and do not have any alternative notifications (such as Toastify) enabled, so the attacking player will not receive any message that they cannot raid something.
So what I was seeing is that the protection is working correctly, it just appears to not do anything because the attacker isn't notified. Can you confirm if this is the issue or we should try and see what else could be the problem?
If you don't think this is the problem I would suggest using the /warmode.tc command to "inspect" what the true mode of the base that you're expecting to be PVE is. Keep in mind that if a base has ANYONE authed on it that is PVP then the entire base will be considered PVP and therefore will be raidable.