For people who watch SteamDB updates, there's been a little bit of confusion on how Valve has been testing titles ready for the release of the Steam Deck on February 25. They've now fully clarified.
The issue surrounds what version they will pick for Deck Verified when games have a Native Linux build. There were a number that appeared on SteamDB, noting Steam Play Proton as the runtime picked instead (meaning the Windows build was used). As example, an update for Portal 2 on SteamDB (their own game) shows the recommended runtime being Proton. Turns out, this was not intended.
Valve shared via email (making clear this was not embargoed info): "early on, there were a limited number of titles that were tested via Proton before Linux before we made some policy changes. Since then all of those titles are already back in the queue for re-testing using their Linux builds".
Additionally, the developer documentation has been updated (right at the bottom) to state:
If my game has a native Linux version and is selected for review heuristically, will the compatibility review take place on the Linux build or under Proton?
By default, we will test a Linux build if one is available. If the Linux build fails compatibility tests or otherwise experiences significant issues, we'll then test the Windows build of your game running under Proton. Our goal is for customers to have the smoothest experience possible on Deck, so we'll submit whichever set of test results is more favorable.
Your compatibility test results will specify what runtime they were generated on. You can see details in the "Details" section of your report under the "Recommended Runtime" field.
If you believe we tested the wrong version of your product, you can always submit for a re-review and specify the platform you'd like us to test.
Something to remember: nothing is final, and even after the Steam Deck releases the Deck Verified program will be an ongoing thing. No doubt there will be changes to how it's run after release too as they continue to try and give players the best experience.