That could be. But, let's consider a hypothetical for a moment. You're behind the gun counter wiping it down, when through the door walks a creature about 6 foot tall and weighing around 180 pounds, with big strong hands and muscular forearms, wearing a dress, panty hose, high-heeled shoes, a fur coat, lots of make-up, and--quite apparently--a wig. Prominent Adam's apple and a deep voice to match. Stops in to look at a high-capacity 12 gauge shotgun. When you call said person, "sir", without thinking, you are informed that you are in the presence of a lady.America is once again showing how weak the country has become.
Now, as an FFL (remember, this is a hypothetical) it is your responsibility to verify the identity of a potential gun buyer. What do you have here? A man in drag? Perhaps.... A convicted felon, who can't legally purchase a gun, posing as a "lady", hoping to pull a fast one on you and the ATF? An undercover sting operation? Who knows?
And what of the I.D. you're shown? Does it identify the person before you as a "man", even though considerable effort has been spent to appear female? Conversely, does the I.D. card identify the person as a "woman", even though you're quite sure you're looking at a guy in a dress and assorted feminine trappings? So, just what course of action do you follow here?
What the inclusion of the "non-binary" category does is render most of these questions moot. The person in our hypothetical can simply check the box marked "non-binary", and that is it as far as your responsibility goes. There is plenty of room in the comments section of the new 4473 form for you to record your observations about men in drag, or felons disguised as ladies, or whatever else it is that concerns you. But it is nothing you have to lose sleep over.