err: D3D9SwapChainEx: Failed to recreate swap chain: VK_ERROR_NATIVE_WINDOW_IN_USE_KHR
Line of interest in log
Try it with the environment variable DXVK_CONFIG=d3d9.deferSurfaceCreation=True.
In my case run ok with dxvk 2.4
Try it with the environment variable
DXVK_CONFIG=d3d9.deferSurfaceCreation=True.
Yes, this fixed it. I can launch the game and play it normally.
The game crashes as soon as I open it. I get this error "DEVICE NOT CREATED 2"

Software information
Enter the Matrix (2003)
System information
Apitrace file(s)
Log files
Matrix_d3d9.log