Quite honestly, I would ask the BATFE and not the experts here on a board.
It is not illegal to have a AR-15 rifle and a pistol and a SB upper and another lower receiver (non-registered as an SBR) etc.. in your home at the same time.
Uppers are not considered the gun, the lowers are the firearms. Just because you have a SB upper in your home doesn't make it illegal if you just happen to have a lower in the same house. It's only illegal when you join the two without going through the tax process.
If you are unsure, then just register one of your lowers as an SBR. That way you can put any under 16" upper on it (or build your own).
But, the main question is if it's illegal to have both an AR-15 pistol and an AR-15 standard length rifle in the same house, the answer is no, it is not illegal (by the feds, you need to find out your own state laws).