Sys;

• Steam Deck (OLED), SteamOS (Stable)
  Affected Games;
• Half-Life, Half-Life 2

Summary;
Simply attempting to change the layout from official to anything else is not possible; any deviation is immediately reset upon launching the affected titles. This issue is not yet present in other Source/GoldSrc titles.
I believe the issue is caused by whatever special version(s) of the Steam Controller API which have been assigned to HL / HL2.

Steps for reproducing this issue:

1. Change or modify the official controller template for Half-Life 1/2 to literally anything else
2. Immediately have your template overridden back to official
   2.5. Your own template is now labelled as 'incompatible' (despite still working fine with every other Source/GoldSrc title)
3. Realize you have no choice but to to press Y to reload
4. Permanently quit playing the affected game(s)