I have decided to create a Mod specific for the Singleplayer that changes only things that are a issue.
The idea is not to make the game esier or something but to fix issues that should not be there in the first place.

If you have any suggestions or remarks please go ahead and share them.

This is the list of things that need fixing so far:
Menu and Settings
Allow to select a screen resolution and fov, this will basically copied from the HZM Coop Mod.

Mission 6 - Engineering
Remove Granade Launcher from inventory as players don't understand what is happening with the splashdamage situation and quickly fail the mission, which makes for a high frustration factor, once you understand what the issue is you don't use that weapon anyway.

Mission 6 - Exterior
Fix gravity bug players drifting in space and not comming down.
Exterior Cannon Primary fire modus not showing pulse beams might need a flushtiki on starting sequence 2 cin.

Mission 7 - Secret Crate Monster
Make crate monster visible using crates or check if player has shadows turned on and temporarly activate shadows until the monster is killed. (If Monster should become visible, this will basically copied from the HZM Coop Mod.)

Mission 11 - Commander fight
The Commander has granades that give a unusuall ammount of pushing force, when the player is hit from above the forces multiplay with gravity some how, killiong players from massive fall damage. This appears to be a bug, there is no indication that it was actually designed and wanted this way, there are other cases where similar bugs happen but non are as servere.

Infotexts/hud could be added to give player guidance on dificult sequences like:
1. Final Boss first sequence fight with the Shielded Control Room, as people often don't figure that one out.
2. Mission 6 Engineering, maybe show a warning hud when player destroys components of the ship
3. Mission 6 Exterioor, maybe show a message when player fires to much on the small ships that keep on respawning

Repository: https://github.com/HaZardModding/HZM-SINGLEPLAYER-FIX

I have published a Alpha Version on Github, this fixed the following issues:
- Reduced kockback of Alien Commander from Mission 11 by a factor of 10 to prevent players getting killed by fall damage rather than the actual projectile damage.
- Removed Granade Launcher from the inventory because it was doing to much splash damage on Engineering Level at Mission 6
- Fixed Crate Monster being invisible on Mission 7
- Fixed Floating/Gravity bug in Mission 6 Exterior

Not yet included:
Custom Screen Resolution Menu

As a player you only need to download HZM-Singleplayer-Fix_Mod_*.zip.
Instrcutions are included.
- The latest version is at the top.
- Click on "Assets" to show the attached files.

https://github.com/HaZardModding/HZM-SINGLEPLAYER-FIX/releases

Just curious, since you seem to be knowledgable about how the game works, do you know what determines the save file location of the game? Is it in a .cfg file somewhere or built into the .exe itself maybe? Reason I ask is I'm trying to play the same save synced between Windows desktop and Steam Deck. Problem is, because the save file is username based, the deck puts saves in a "deck" folder, while my desktop puts it in a different username folder for that machine. I can copy files back and forth, or even sync local folders, but it's a hassle that I'd like to avoid if possible!

The place it is stored in is deccided by the operating system, depending on the file privileges.
What you can configure is the name.

You can create a shortcut on windows and then add these parameters:
+set config "deck.cfg" +set username "deck"

You will have to make a copy and rename your current CFG and save-files on windows.

Also make sure you set in the CFG file or input it via Console:
seta r_primitives "2"

That did exactly what I needed, thank you so much!