UE4Editor load .ini files accroding to operating system but not cooking platform.

This is a known issue, which is still present in UE5.

A workaround I’ve found is to create a file Config/DefaultPakFileRules.ini.
See instructions in the Engine’s version: \Engine\Config\BasePakFileRules.ini

You can exclude folders of content like this:

[ExcludeContentForWindows]
Platforms="Windows"
bExcludeFromPaks=true
bOverrideChunkManifest=true
+Files=".../Content/<YourGame>/Folder/Path/*"

The files are stripped out post-cook.
To verify it worked, you can double-check that the files you want to exclude are NOT listed in the AutomationTool’s list of pak items in: <Engine>\Engine\Programs\AutomationTool\Saved\Logs\PakList_pakchunkX-<Platform>.txt

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