While it's possible to set a file association for css, it doesn't seem to apply (double-click still uses the RH style editor). You could raise a bug report using the link on the right-side of the Overview page of the forum.
I normally edit using the in-built HTML editor using right-click > Edit With > HTML Editor. This shouldn't make any changes to your stylesheet that you don't manually enter. However, if you accidentally double-click on your stylesheet and open the Styles dialog box, then RH will play around with your styles. Mostly just breaking up @media sections into individual definitions. But I can imagine that some of the more advanced features, like your font fix stuff, may be removed because RH doesn't understand it.
Having said that, there is a new version out which you could check to see if changes have been made.
I agree that the File Association should work differently. I've always felt that double-clicking a CSS should open it using what you specify here.
In my experience, what you configure here is used when you right-click the CSS in the Project Manager and choose to View.
One way to ensure that you end up with what you want is to maintain a separate copy of the CSS file and specify it in the Single Source Layout recipe.
Ha! I never, ever thought of using View!
Just to add: RoboHelp doesn't like too advanced CSS. Even if you create it with Notepad, RoboHelp may rewrite some CSS anyway (such as ::before, vendor prefixes). RH2015 does a much better job at keeping your CSS intact but even then it will break up combined selectors.