I hear roofing your pens works against bats.

But unless things have changed the raid mobs go after you, not your base. If you are in or near your base it and its contents can fall victim to the baddies as a sort of collateral damage.

In my experience if I lead them away from my base (but still stay within the red 'raid' circle marked on the map) I can fight them with little risk to my base and its contents.

Again, maybe things have recently changed and I am unaware of it, but so far fighting raids away from my base while still in the circle has worked.