No problem with what you want to do.
Buy your lower, decide if you want to do it as a trust or individual - have the lower engraved with your or your trusts info, city & state you plan on making the SBR in.
Send in your Form 1 to BATFE either by mail (individual) or via EForms if you go trust. On the F1 you must declare caliber, barrel length & overall length, and you should build it to those specs the first time once you get the approved tax stamp.
From that point on - you can buy/make as many uppers as you wish - change calibers, change barrel lengths, etc... The BATFE "suggests" you inform them on any permanent changes, but it is not required (at this time, anyway).
I have a AR pistol with both a 5.56 & 300 BLK uppers - my F1 for a different lower has been submitted as a 10.5" 5.56, but will be using both on the SBR once its been approved. I also plan on a SBR 22LR upper...
Decide what you want, and get in the pool!
Take care,
Bob S.