Just so you know, I have been using both War Mode and Raid Protection together and it is working well for the most part. My goal is to offer offline raid protection to all bases where a PVP player is not online.
I cannot disable War Mode protection because I need it to protect the bases of PVE players when they are online. Raid Protection isn't able to add online protection to only PVE players as far as I can tell. So, right now PVE bases are double protected by War Mode and Raid Protection when PVE players are offline, which is fine.
I can give the raidprotection.ignore permission to the "warmodepve" group so that if a PVE player is online it does not disable offline raid protection for the base, thus requiring that a PVP player be online in order for the base to be raidable. This works how I want, but there are 2 issues with this approach.
1) If the TC was placed (founder) by a PVE player, then the base has no raid protection at all because of this bug with Raid Protection: https://codefling.com/files/support/16917-offline-protection-not-working/
2) If the player switches to PVE or to PVP, the raid protection is not updated automatically unless the plugin is reloaded because of this bug with Raid Protection: https://codefling.com/files/support/16868-ignore-permission-not-working/
It would still be nice if the Raid Protection plugin was updated to integrate with War Mode more easily, but if these 2 bugs were fixed it would address my use case and allow your customers to add offline raid protection to War Mode and solve for the issue of bases with both PVP and PVE players on the TC.