It is very very simple.
If you want inner hull slots to be damaged right along with outer hull slots when the damage sweeps past, then change all the inner slots to outer slots in your layout!
Inner slots really don't make much sense the way stock uses them (but then again a lot of stock stuff has never made much sense)
What Inner hull slots are actually useful for are abilities which you want:
A) To look like they are built in to the hull. (And don't take damage except maybe from special weapons)
B) To be optional. (User can pick and choose without cluttering the vehicle list)