The Flatpak package of Steam is not officially supported by Valve, so I don't see the point of mentioning a quirk with where it stores Proton logs here.
Whether or not Valve 'officially' provides a Flatpak manifest is a moot point. Flatpak users are still Linux users and Flatpak isn't a blocker on games running on Steam. See: the sum of ProtonDB Reports and Compatibility Reports Issues listed here.
It's a minor line edit to a template to help improve feedback which is in Valve's interest to make reporting easier for increasing Steam Deck compatibility, etc. It takes all of 30 seconds to improve and no unit tests to worry about. There are numerous distros that ship with Flatpak out of the box, promote it, and will have users install Steam via Flatpak: https://www.ubuntubuzz.com/2021/10/distros-which-adopted-flatpak-in-2021.html
Valve has even promoted the Flatpak of their Steam Link app in the last year: https://steamcommunity.com/app/353380/discussions/10/3106892760562833187/
make a PR
I'm surprised that Flatpak redirects $HOME. That seems like something Flatpak users should be aware of, since it'd affect a lot more than Proton log locations.
Nothing extracted yet.
Problem:
Currently the Compatibility Report Template does not include the filepath for the generated .log if Steam was installed via Flatpak:
Solution:
Update the instructions to reference Flatpak filepath (~/.var/app/com.valvesoftware.Steam/) so something like: