These doors are specific to the BEOD and the SECM type truck bodies. They have a lip on the upper edge that puts them behind the roll down door, sealing out weather and securing the door from opening when the roll door is down.
If you just have the filler panel, then yes, that area is going to be closed off and unusable for normal operations.
edit: the actual setup for the BEOD removes the seat base and the TCM mounts onto a special bracket that also has the storage location for explosive primers or so I have been told. I just know that door has a lockable latch, and so does the roll up door so you'd have to unlock two seperate locks in order to access.
