I think this is actually a fshack bug, as it doesn't invalidate swapchains when fake resolution changes. The dxvk swapchain change caused the regression but probably because of a different swapchain recreation strategy.
proton 7.0x1 2023-02proton experimentalx1 2023-02
Bisected to the https://github.com/doitsujin/dxvk/compare/aca67f64...76e6b276 range, it can be reproduced with Proton Experimental where it is broken, and Proton 7.0 where it is working fine.
With a 1920x1080 native monitor resolution, when selecting 1920x800 the display is stretched vertically in Proton Experimental, and correctly padded with Proton 7.0. I can reproduce it as well right on game startup if some non-native resolution was saved in the game settings.
System information