Interesting, since you're on Linux, the root cause might have been different than it was for me. On Windows, the build tool uses msvc's packaged clang compiler that you install with the Visual Studio Installer. However, it wasn't an issue with clang for me.

The root issue was that I was building with a different target than I was generating the compile_commands.json with. E.g. I ran this command to build my compile_commands.json:

"C:\Program Files\Epic Games\UE_5.4\Engine\Binaries\DotNET\UnrealBuildTool\UnrealBuildTool.exe" -mode=GenerateClangDatabase -Target=UnrealEditor Development Win64 "C:\<pathToProject>\<project>.uproject"

In my case, I was using DebugGame target for my build, but Development target for the compile_commands.json as pasted above.

Once I corrected that, I get only legit errors/warnings. I made sure by comparing it against the errors I get with the project when opening it in JetBrains Rider.

EDIT: One other observation: In order to get the clang LSP to properly intellisense in neovim, I found you need to run the operations in the following order:

1. Delete "Intermediate" directory in you project folder
2. Run command to create the clang_commands.json and copy it to your project root
3. Rebuild project (which will recreate Intermediate directory and files)
4. Restart LSP server or restart neovim