What happens when you run your generated help output through your customized CSS at the time of generation (done in the SSL recipe)? Does RH still try and modify it?
No, it does not modify the css file in that case. Actually, it also does not modify the file if you only set the properties of a topic to use the css file (I just tried that). It only alters the css file as soon as you open a topic using that css in the RH editor. So if I never edit any topics, I'll be fine
This CSS rewriting is an annoying habit of RoboHelp. Nothing to do about it that I know of. Personally, I use a script to always copy the CSS from an external location into the output whenever I generate.
You can leave sub and sup out of the css since all browsers will display them correctly aligned in a smaller font. Only the RoboHelp WYSIWYG will show the sub/sup with the regular font size.