I'm going to think out loud here, for whatever it's worth (maybe nothing?)
There could be a million reasons they didn't put a dual stage air filter on a BX. Cost being one, they try to keep cost down-yet still maintain a reasonable lifespan while at the same time being able to outsell the competition and turning a profit. Manufacturing is a pain in the butt especially when it comes to this kind of thing where competition is cut throat.
Secondly (again just thinking out loud here), on BX's with the engine turned around backwards, radiator in the middle, they already have a tendency to get warm. Combine that with owners that don't always know how to take care of their equipment, and you have a disaster waiting for a place to happen. On diesels, the ONLY thing that cools the tops of the pistons off is a litlte oil splash from underneath, the piston rings (rings tranfer heat into the cylinder walls where it's carried away by coolant..) and by a large margin, the AIR that is drawn in from the atmosphere. Now what if we added a second air filter element, thus creating some restriction, resulting in a little less air entering the engine? Now we already have an engine that runs warm, with owners that don't always know how to maintain the radiator/screens/belt, and if we reduce the amount of air going into the engine, we can potentially get even further into overheating. Obviously that's not ideal. Nobody wants that.
I asked the kubota service rep about it once and didn't get a straight answer. Imagine that.
A lot of standard L series tractors don't have a inner element either. The grand L's do, or at least all the ones I've dealt with did. B series? I don't remember them having an inner element but I think it was an option.
The inner element don't catch squat for dirt. All it does it keep the pieces of the outer element from going through the engine should the outer fail for whatever reason.
If you're worried about it run the engine for 100 hours on an oil change, and send some oil off to blackstone and see how much dirt's in it. If it's concerning, look at several areas: Your funnel, the crankcase vent, and the air filter/intake system. That's why those are listed as service items in the WSM and OPS manual. I've seen a clamp screw back out on an M9540 and dust a turbo, to my knowledge the motor's still kicking though. The turbo compressor wheel was trashed.