Yes, you can buy the "L" shape stems. They're available anywhere that sells parts. You can try e-bay, too. Of course, I've been lazy lately and just using my dealer to look for everything for me
It's interesting, though, because all of the Agility 125's in my local shop that are new (including mine), came with the straight stems. And I thought the same as you, that the "L" stems should have been placed in so filling the tires was easier.
I've debated getting the stems, too, but it isn't too much of a pain in the rear to just deal with it for now, ya know?
Have a great week!