First and second controller swapped in Flatpak Steam

**Game information**
Every game I have tried so far.

**Distribution name and version where applicable**
Parabola GNU/Linux-libre (rolling release).

**Flatpak info**
Flatpak 1.10.1
default
host

**Problem description**
I use an [EMS USB2](https://www.amazon.com/EMS-USB2-Sharp-Shooter-Compatible-PS3/dp/B008FG72X4) with two PlayStation 2 controllers attached. In Flatpak Steam the controllers are swapped in every game I have tried. Every game with full and partial controller support is consistently affected. The order of the controllers is swapped even in the Steam controller settings. The first controller is detected as the second controller and the second controller is detected as the first controller.

**Does this issue reproduce with native Steam**
Curiously the issue does not reproduce with native Steam.