A player has multiple buildings. One is protected and another one isn't. However, the base that isn't protected was 99% created by them. Another player created a wall or two.

Will it not protect a building if even a small fraction of it was built by someone else?

I did some testing and it appears that's the case based on "Check full ownership of the base instead of only one block": true,

For protection to exist, the structure has to be completely owned by that player who has permissions. 

Great work here! Love the plugin!