libei is the only way a flatpak is allowed to send inputs to a Wayland desktop. Anything steam does to interact with the desktop or another application via Steam Input would trigger this. Patching it out is not an option because he would be opening yourself up to remote control attacks.
You would have to convince everyone that a whitelist for a single application is an acceptable compromise. What we do in Bazzite is we ship extest which implements the XTest API through Wayland. This solves the problem but is not applicable to the flatpak.