because its a pain in the butt to have to edit a text file to change settings, insert new disks etc.. Dont know if that functionality is there since the last time I used it.
There is now FS-UAE launcher which is supposed to give a WinUAE style interface for configuring options, Ive not used it tho as I just have a A4000/040 setup with AmigaSYS and WHDLoad games so i just setup it up once and be done with it.
Floppys can be easily mounted via the bulit in gui.
Also, as said if not tried WinUAE via Wine is another great alternative although I have always had issues changing between native & p96 graphic modes on the fly...