The issue is that the website is facilitating beer sales to the final customer and taking a cut of what is received, which sounds like retailing. The website is doing business across state lines which makes it subject to federal jurisdiction, hence the TTB involvement.
A retailer profits from the purchase and sale of product. The website isn't buying anything, its just providing a service to the brewery. The more times the service is provided, the more profit is earned. Seems more like the "Square" app used by Tasting Rooms to accept credit cars.
+1, if taking a cut of monies earned by selling alcohol were any different than any other sale things would be very difficult for credit card processors, payroll processors, tax preparers, delivery companies...