I can't fill in all the details of what's inside the smokeboxes, however a couple of observations I've made. In a lot of cases, the smokebox was initially extended with a bolt on (rivet on maybe) extension. This usually coinsides with the disappearance of the diamond (or whatever shape) stack the engine was originally equipped with. This suggests some sort of internal spark arresting sort of dealie.
Subsiquently many engines received new boilers to replace their original iron boilers and it seems to me that at that time they also received new smokeboxes, which centered the stack to the middle of the top of the smokebox (rather than the middle of the original smokebox course). This might explain why on many engines the smokebox seemed to get longer, the stack remained centered in the original smokebox and a new course added in front of it, then shorter later, with the stack moved forward along the top of the smokebox.
Don