With the Steam Play Proton 5.13 compatibility tool being a major upgrade, along with it now using the Steam Linux Container Runtime, it did come with some annoying issues that they're now trying to solve.
One of the problems was that since the Windows games are contained and isolated from your system, you couldn't then run tools like MangoHud or the post-processing layer vkBasalt. Valve have now updated the container systems, to allow them to import Vulkan layers from the host system.
They also noted this about the new way it works:
The container does not have the same /etc or /usr as the host system, so not all system-wide configuration files will be available. For best results, use a configuration file in your home directory. Alternatively, there is a new environment variable PRESSURE_VESSEL_FILESYSTEMS_RO which can be used to pull in configuration files from other directories (although not /usr for technical reasons): for example you could use PRESSURE_VESSEL_FILESYSTEMS_RO="$MANGOHUD_CONFIGFILE:$VKBASALT_CONFIG_FILE".
If you wish to try them out, you need to opt into the Beta of the Steam Linux Runtime and the Steam Linux Runtime - Soldier (the newer one), selecting the "client_beta" option from the dropdown.
For best results, you should also use the Steam Client Beta too.