Hello, this is a good question, indeed.
I didn't found anything in the fs-uae docs to disable shaders for rtg modes.
Maybe you could ask in the upper level:
http://eab.abime.net/forumdisplay.php?f=122
Or, with a github account, asking upstream by opening a feature request here:
https://github.com/FrodeSolheim/fs-uae/issues/new
Let us know!