Steam downloads the Windows version of a Proton-enabled app, but still stores files in the familiar `~/.steam/steam/steamapps/common/[appname]` directory. On first launch, Proton provisions a Wine prefix (created in `~/.steam/steam/steamapps/compatdata/[appid]` by default) that holds pertinent state data and a basic Windows filesystem in `$WINEPREFIX/pfx/drive_c`. This filesystem is presented to the app as its root Windows filesystem. Save games are usually stored in the prefix as well, making save game import [complicated](https://www.brainvitamins.net/blog/mass-effect-savegame-import/).
Steam downloads the Windows version of a Proton-enabled app, but still stores files in the familiar `~/.steam/steam/steamapps/common/[appname]` directory. On first launch, Proton provisions a Wine prefix (created in `~/.steam/steam/steamapps/compatdata/[appid]` by default) that holds pertinent state data and a basic Windows filesystem in `$WINEPREFIX/pfx/drive_c`. This filesystem is presented to the app as its root Windows filesystem. Save games are usually stored in the prefix as well, making save game import [complicated](https://www.brainvitamins.net/blog/mass-effect-savegame-import/).
Windows applications frequently have additional dependencies like the [Visual C++ Runtime Redistributables](https://support.microsoft.com/en-us/help/2977003/the-latest-supported-visual-c-downloads), and apps may require specific workarounds to run well in Wine environments. Many of these concerns are managed by the app's install script (usually `~/.steam/steam/steamapps/common/[appname]/installscript.vdf`), but `~/.steam/steam/legacycompat/iscriptevaluator.exe` also runs inside the Wine environment during initial provisioning and appears to manage Proton-specific dependencies and tweaks.