Seems like this happens only when launching the game in fullscreen mode. The game launches fine if set to windowed mode. On a side note Just Cause 3 also doesn't launch properly if you allow DXVK to be promoted to DXGI.
Unfortunately presentation using DXGI interop is entirely done by the driver. We don't have any influence on it at all so there's nothing we can do problems with it.
After reading this topic here https://github.com/doitsujin/dxvk/issues/5258 I got curious and tried to experiment with window styles a little bit.
Looks like removing WS_CAPTION and WS_THICKFRAME from window style prevents the game from crashing:
https://youtu.be/cg0fqmVYJ_c
Just FYI
Under normal circumstances, Just Cause 2 runs just fine when using DXVK (version found in this link: https://github.com/doitsujin/dxvk/issues/5172#issuecomment-3243026244, also tried the latest stable version 2.7.1), but when I set nVidia's Presentation Model on the game's driver profile to "Preferred Layered on DXGI Swapchain" and use the appropriate Presentation Model flag that allows DXVK to be promoted to DXGI (in order to get Independent Flip, and thus VRR support, without having to set dxvk.allowFse = to True), the game has a white screen at launch and becomes unresponsive. (can't get a screenshot of said white screen)
OS: Windows 11 24H2
GPU: nVidia 3070
Driver version: 580.88
JustCause2_d3d11.log
JustCause2_dxgi.log
If this can be fixed, that'd be great. If not, well at least dxvk.allowFse= True works without issue.