but have you ever have a Amiga? you should know that all games must remain like old 4:3 TVs. black bars are necessary.
Considering, I was a TV engineer and owned a few amiga's. Yes I have Amiga's and could not care less about 4:3 personally, games look as good to me in 16:9.
I would love to see the feature we added to PSPUAE, called Auto zoom. Basically, you set it to stretch, it then works out where line starts and ends. Removing ugly borders from all games, like turrican. Full wide screen bliss,

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However, I have just answered your questions. Its not the GS causing your issue.
Have you tried adf version? as it works 100% perfect in 4:3.
WHDBoot archive, which I'm guessing is the same as yours, forces it to 16:9 and ignores what GS is set to. I could ask for fix to stop anything altering GS Amiberry config.
As I wrote I am not using the function stretch mode
Please read what I posted, you seem to ignore the important parts of my posts.
What ever your using is FORCING it to stretch. Its overriding GS settings.