Big thanks to Uni on the VNWiki Discord for figuring this out.
Problem
The d3d9.dll provided by the Todokanai fan translation enables subtitles for certain scenes, such as the one below. Disabling the dll removes the feature.
Solution
Disable DXVK and use WINED3D + the DLL override instead.
Video conversion + GE Proton is still required for videos to work, tested on SteamOS with GE-Proton10-25
Required launch option:
PROTON_USE_WINED3D=1 WINEDLLOVERRIDES="d3d9=n,b" %command%
Tested on:
SteamOS 3.7.16
ROG Ally Z1E
GE-Proton10-25