Of the four KTM's I have owned I've never once had a problem getting the air filter seated properly. Although I have seen a freshly rebuilt sx150 engine get destroyed within 3 hours of riding because he didn't put the filter on properly, so I guess you could put them on wrong but if you take care when refitting the filter you should be fine.
Actually been wondering how hard it would be to put a KTM rear end on my CR5. It seems like a pain in the ass now having to remove the seat all the time just to change the air filter.
Nothing like as much of a pain in the arse as jerry rigging the KTM rear end to the CR500 would be, put it that way You'll get used to the seat thing, and its nothing compared to changing the air filter on a 10-13 YZ450F. That was absolutely ridiculous.
Ye I figured it would be pretty difficult but I doubt I'll be selling it so I'd like to try and get everything perfect on it, besides apart from the subframe I already have most of the parts that would be needed lying around the garage.
I have seen a service honda airbox with a door on the side but that was an 09-12 rear end and to be honest it kinda crap in comparison to the KTM setup.