It all seems somewhat grey and ambiguous, so YMMV.
Obviously, you can own an AR pistol and an AR rifle at the same time - I don't see why that causes a problem. The fact that you could THEORETICALLY take both apart and swap the uppers to create an SBR is no different from the fact that you could just as theoretically take a hacksaw to your shotgun and create an SBR. Both are relatively easy to do, but there is no crime until it is actually done.
If you own an AR rifle, and an AR pistol with an extra pistol upper, then some people might start to worry - although I don't think I would personally. I have a registered SBR, and I feel like I can buy a 11.5" upper in addition to my current 10.5" upper, and not worry about it.
If you own an AR rifle, and an AR pistol with three pistol uppers, and just happen to have two extra complete rifle lowers lying around, then you probably want to be wary of inviting numerous BATFE agents over for dinner and showing off your collection of uppers and lowers.
I personally don't think that the BATFE is actively looking for people to bust, unless they are assmbling a pistol upper on an unregistered rifle lower, and taking it to the shooting range, or something like that. However, IF you had several extra pistol uppers and several unregistered complete rifle lowers lying around in your house - and you got raided for your post-growing operation in the basement, then I have no doubt that the BATFE would charge you with something.