Why is there an option for two 12.9" size screenshots in App Store Connect?

If you take screenshots for the iPad, in the screenshots for the iPad Pro 2nd generation the device should be with the home button, and for the iPad Pro 3rd generation - without the button.

As previously mentioned, if you are adding device frames to your screenshots, the frames must be different. The 2nd gen has a home button, the 3rd gen does not.

Additionally, the actual screenshot from the 3rd gen has the gesture bar covering your app, the 2nd gen will not. I would expect Apple to refuse screenshots claiming to be third gen without the gesture bar, unless that's how it appears in your app.