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.
What's the 4:3 situation when starting WHDLoad Games (with JST?) on Amibench?
I have no A600GS yet but this is an important aspect for me. IMHO 16:9 strech graphics look absolutely horrible.

Good to know that using ADFs bypasses this, but let us be honest - many ADFs are badly cracked games with glitches, graphics corruption or some other flaws which make them crashy or in the worst case make the game un-completeable. The WHDLoad-installed versions do have fixes for glitches in the original game on the other hand. So I prefer the WHDLoad-versions very much.
So I would also vote for a fix that the GS Amiberry config always should be respected.