This "fixes" the "always 3 Overlays" problem experienced on Linux / Steamdeck, when using Racemenu. Source of the error is a parsing problem of the " ; COMMENT" entries. Put this here mostly for visibility, if someone else experiences the same problem, the fix is easy to do yourself.
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Apparently, Linux / Steamdeck has a problem with parsing headlines in configuration files, if they are followed by white-spaces or comments. The solution is to put the comment in a line of it's own.
Specific entries (like iNumOverlays=3) are fine with trailing whitespaces / comments, it's only section headers that are problematic.
The file provided can replace the default skee64.ini, though if you did any changes there, you have to reapply them in the overwritten file.