It is interesting how KTM has a series of running changes to address the issues associated with oil changes on these beasts, like the mods to the frame and different gasket. I now understand why there is such variation in people's experiences - I thought it was mostly individual's particular tolerance for mechanical difficulty, but it is more variation in each bike.
Mine is an 00 and it has the "oval" frame tube which is a tight clearance, AND it has the crappy o-ring seal. Because of both, I find it makes a lot more sense just to remove the banjos completely, so that all I'm doing when I put the cover on is placing the filter in the recess, fishing the cover into the slot, and then pushing it down carefully, keeping the cover as perpendicular to the mating surface as I can. But I can see if you had a little more clearance and weren't so worried about pinching the o-ring, that leaving the banjos on would be fine.
Another tip on the o-ring: make sure the groove it fits into is clear of debris (or gasket sealer if someone PO has mistakedly used same). Only then will the o-ring fit down into the groove and be held down by the little nubs in the groove designed to keep it in place. Having the o-ring stay in place is critical to avoiding pinching it. If you pinch it, you're toast.