A unique css file is created based on the form design that you choose. Most people would want to use the same css for each form on the site and wouldn't want repeated css files. I see your point, since you are customizing the css in the file that you wouldn't want it overwritten. I usually solve that problem by not editing the css file created by the form builder and I overwrite attributes in a separate css file for any design changes I want.
A compromise might be to not overwrite the css file if it already exists. That would allow you to use the css file and not worry about it being overwritten without the clutter of separate css files for each form. The issue with that is that if I was ever to do a bug fix or css update it wouldn't update on your site unless you manually delete the css file first. That might be an acceptable limitation for the benefit of being able to edit the css file.
I'll consider adding logic to not overwrite existing CSS when running the wizard, but I'd suggest using a separate CSS file for edits in the meantime.
