IIRC they aren't based on Flatpak, they existed even before Flatpak gained any traction. I actually do think Steam changed a few things in pressure-vessel to be more similar to Flatpak, but they mostly evolved independently.
The main reason I think they are pouring money into Flatpak is because that is the main way to install applications on SteamOS (that aren't games shipped via Steam).
Well, it sounds pretty funny.
What can be said factually is that the Steam Deck is based on an immutable distro like Bazzite, which is a lot more important than flatpaks themselves. Flats are just a popular way to get apps on such a setup. I see a lot of resistance to them in general, not just in specific individuals or communities on the web, and they're actually pretty solid and do see lots of investment from other companies. SteamOS itself being an immutable distro, Gabe is indeed at least indirectly shitting his yacht money into them.
[1] https://gitlab.steamos.cloud/steamrt/steam-runtime-tools/-/b...