I'll take a look. I can go through the RaidableBases plugin and work on an update for MLRSDamage that integrates better with it. When I first coded all of it, it was when MLRS was new and RaidableBases hadn't addressed it yet, so there integration wasn't possible at the time.
Inside of MLRSDamage, the line for "Allow Damage to Raidable and Abandoned Bases" just checks to see if the building blocks being damaged have an ownership of "0". This is regardless of who "owns" the raid, for those PVE raids, where you don't want someone else doing damage to the base. This is what I can work on to integrate with RaidableBases.
It does the other checks however. So if Damage to Players is off, then maybe the line in the RaidableBase profile "Allow Players To Use MLRS" is somehow overriding it and allowing player damage.
But first, maybe see if setting "Allow Players To Use MLRS" to false in your RaidableBases profiles fixes the issue? I'll work with the author of RaidableBases to see where conflicts may be coming up, but theoretically, if MLRSDamage has Allow Damage to Players as false, but players are taking damage, then some other plugin must be overriding MLRSDamage.