I've brought two iPhones in for battery replacement and both times my phone left with additional issues. One issue required replacing the phone. The other was a minor annoyance with the screen.
Yup I only have done this once for my iPhone 6+. I left with more issues and returned to apple store. Apple replaced the entire internals from screen to motherboard. The only thing that was old was the aluminum casing.
If you have the battery replaced using the official channels you have warranty, both on the new battery and the repair.