Backstory: I ordered two different firearms, one was back-ordered and the other was much later but in stock. Both were shipped to different FFLs, from different retailers. However, they both are ready for pickup on the same day, which means my background checks will go through for two different firearms on the same-ish day.
The ATF gets notified when the same seller sells multiple guns within 5 business days to the same buyer, but is there a problem if I run background checks for two different guns on the same day? Can I get a knock at my door in a week by a glowie?
The gayTF isn't notified unless you purchase more than one handgun in a 10 day period, more than 5 guns at once, or some combination of that. The most you'll get is a call. You should be fine at either place, granted you're fine at all. It shouldn't matter.