Bluejack, yes you can own multiple uppers with a registered SBR lower, you write what bbl length and caliber you start out with on the form when you build it. I'm not sure if you have to inform ATF of any other uppers you acquire to use with the one lower. Normally if you change the bbl length they want a note saying that so they can amend their paperwork, but with the AR being so modular and popular they may not want the additional paperwork load.
As for the rest: Basically, the TC decision set forth a legal test for whether or not a "group of parts" was considered an SBR if they were not assembled as such. The gist is, if you have a legally registered SBR lower or a pistol those short uppers can be attached to, a pile of them sitting in your garage looks like spare parts for your SBR or pistol, assuming of course you have never attached them to a normal rifle receiver. However, if you don't own an SBR or pistol lower there is no legal way to assemble that group of parts and the only way to assemble them is in fact as an SBR, then the constructive possession thing pops up.
It might also pop up if say you stored a spare pistol upper in the same case as your regular AR rifle instead of the pistol case. Sorta like it's legal to own a hacksaw and a shotgun, but it kinda gets iffy if you wrap some masking tape around the bbl at the 14" mark and put a dotted "cut here" line on it and leave it on your workbench next to the saw.
As far as homemade receivers go, if you make it a pistol and it doesn't have a buttstock, no problems. It's a pistol. OTOH, you own one pistol receiver, no rifle receivers, and have a buttstock handy what does that look like? Even owning the parts along with an unfinished receiver may be a problem, people have been busted for owning a STEN kit and a plain steel tube with a cutting template glued on.
Not illegal to buy a short upper for a pistol, or as a registered SBR. However, as 4th has pointed out recently some companies won't sell to you unless you send them a copy of your SBR paperwork.
Bottom line, jump through the hoops to be legal.