I see no reason to believe that Nike ever intended to use this app to help the customer. Everything about the app is set to provide with an absolutely treasure trove of information. Store your credit card number? Store your billing address? Store your mailing address? Your name? Your e-mail? Your shoe size? What types of Nike products you prefer? What types of Nike products you buy? What is your cell phone number? Type of phone? Billing account tied to your phone? Area of phone usage?
Every one of those things I listed is something that Nike can use to market to you, sell your info, start clamping down on bots (not completely, but build a much stronger "mapping" of where their product goes) if they ever actually want to, and figure out where products are selling. If the app produces heavy traffic from specific "rural" hotspots, they can target shipments to those markets. It can greatly improve their efficiency while vastly increasing their knowledge and access to their target markets and help them control what shoe goes where.
Beyond the app, I'd be surprised if Nike is dumb enough to not be already scanning each unique pair prior to shipment. If each shoe is given a unique code and they track that code, they can monitor where the shoe actually ends up when it's on the internet. Pretty easy way to figure out the end location that way instead of trying to cut the heads off of all the offshoots.
Of course, this assumes that Nike has any true interest in anything, which they don't because they make $12 billion easy every year in straight profit. So, lol jk wtf omg bbq at all of us.