I believe I've accidentally selected 1920x1080**x16** mode instead of 1920x1080**x32**, as I managed to break it again... So it's not the Proton issue.
I've fixed it by uninstalling Il-2, *and* manually removing leftover directory `.steam/steam/steamapps/common/IL 2 Sturmovik 1946`. It launches now! Maybe I've changed some settings in the way it made it to break?