I don't think that the target distro for the Valve's Steam client package and what distro SteamOS is based on are really related the way you're suggesting. For starters, the Steam client package Valve provides is for Ubuntu, and SteamOS is based on Debian, as you say, so it's not like they're the same today either.
By providing a Flatpak, instead of a package that's suitable for some other single distro, they dramatically increase the number of Steam users who are going to be able to use the Valve provided package instead of some repackaged version from a third-party repo, and they're no longer at the mercy of bad decisions made by the any single distro.
In any case, if having the environment the Steam client is run in and SteamOS be similar is a goal, Flatpak actually gives them a way to do that much more effectively. If they maintain their own Flatpak runtime based on the SteamOS userspace, then everyone using the Steam flatpak will be running it in an environment almost identical to SteamOS, regardless of what distro they use.