Once you have your stamp, the gun is registered and contained in their database with your serial number as an SBR. The unit first has to "be" an SBR to fall under the SBR regulations. If it is not an SBR, then it's simply not an SBR. The fact that it is on the db allows it to be configured as an SBR but if you don't configure it, it's simply not an SBR. If you'd like, you can always send a letter in requesting they remove it from the database. This is also the way you might sell this weapon in the future without having to have the purchaser get his/her own stamp prior to taking possession. Think of it like this - similar with a solvent trap you might purchase. You don't drill the holes until you receive your stamp. Once you receive your stamp, you are now allowed to drill the holes, ensure the proper markings on the can, and now the solvent trap becomes a suppressor and is an NFA item. Prior to drilling the holes, the can is not a suppressor, it's still a solvent trap. Solvent traps are not illegal to possess or transport. Hope that helps. It's been a while since I researched and read through everything, so unfortunately I can't point you to the black and white version.
If I remove my stock from my Scorpion, and it has no stock what so ever, ask yourself if it's a pistol or an SBR. The database that allows it to be an SBR isn't a searchable database or something readily available to do checks with - so it would be far fetched for ATF to be sitting at your range asking each person with a Scorpion in pistol configuration (or an AR type gun) - sir, I know that's not an SBR right now, but are you sure it's not on the NFA database having been provided a stamp to make it an SBR?