There is only one config. This config is modified on the fly for the individual games.
Well, my memory tells me that there's some command-line options
working even for WinUAE. So ideally, you wouldn't need to use ANY configuration file, merely a huge sequence of command-line options.
Hmm ... I had a quick look at Toni's latest source tree but unlike a couple of builds before, the entire docs tree is removed.
You will not find the full list of command line options unless in the Linux UAE docs.
Attached is the file 'README' from original (!) UAE 0.8.22 by Bernd Schmidt.
Look for "Invoking UAE" (Line #124 ff.
), these options should work with WinUAE as well!