Those log messages are not a problem, I can also see one line in the log that indicates something is going wrong:
3521.478:012c:02c8:err:vkd3d-proton:vkd3d_queue_flush_waiters: Failed to submit queue(s), vr -4.
I suggest you edit the issue title with what the actual problem with the game is (i.e. crashing/freezing).
For further debugging, downgraded drivers from 545 to 535 which solved the failed to submit queue errors, however, what has remained is this error:
4224.003:012c:026c:err:winstation:map_shared_memory_section failed to open section L"\KernelObjects\__wine_thread_mappings\00000148-input": c0000034
Despite the "solving" of the submit queue errors, no further progress has been made in the dropship scene, crashing at roughly the same point.
Note: this log was submitted under GEProton 8-31 but persists again through hotfix, experimental, and proton8
steam-553850.log
I have a very similar problem to yours running Fedora 39 KDE on my RX 7900 XTX
I am also sharing the log in case it can be of use, this one is tested using Proton-Experimental and no other launch parameter
proton experimentalx1 2024-02
Been attempting for the last few days to get Helldivers 2 to run on latest version of EndeavourOS with a 5800X cpu and RTX 2070 GPU with little success. I have attempted nearly every version of GE proton and official steam proton versions and all get to the exact same point (https://youtu.be/MSyFUkMi9E0?t=161 Not my video, merely a timestamp to show point of failure, give or take 10 seconds) and will freeze, with audio playing for another 5-ish seconds before cutting out entirely. To rule out that it wasn't a complete DirectX12 issue or VKD3D issue, test case was run with Dead Space 1 Remake which ran well enough (60+ fps, no crash with ~2 hours of gameplay)
Software information
Helldivers 2, appid 553850
Settings are default as I cannot get past this initial cut scene, however, I have tested this with a config file from a friend which had all settings at the lowest possible value which resulted in the same issues.
System information
Log files
steam-553850.log