Getting in a normal boat as an Enderian protects the player from the water the boat is in. This effect is not replicated with the boats from the mod Small Ships Mod (https://www.curseforge.com/minecraft/mc-mods/small-ships).

If this cannot be resolved easily, I would suggest a configuration option of rideable entities that protect from water damage.

Unfortunately, this issue isn't on my end and adding a config would only hide the issue.
Please ask them to fix it (It can be done easily by using a mixin at Entity#updateWaterState@HEAD).