Apple maintains it is very sensitive regarding its equipment, even in the after sales service. The Cupertino company Genius desk may refuse to make certain repairs if certain criteria are not met.
One of these criteria was related to the iPhone battery. If you brought an iPhone with a third party battery, the Genius counter would refuse to make any repairs. However, it looks like a new Apple policy will change that.
According to MacRumors reports, users may already have their iPhones repaired at the Genius counter, even with third party batteries. This confirmation officially came from France, where a store had applied the new policy. However, the decision was suspended for work safety concerns.
Apple becomes more tolerant of repairing third-party battery iPhones
With respect to your home country, Apple will reflect this new policy also in US stores. The information came from 3 different sources near Cupertino's company.
In this regard, Apple's new policy allows Genius counter employees to replace third-party batteries with delivered iPhones. If the repair is battery related, employees must discharge the battery below 60%.