With a bit of creativity, you can (sort of) do this already using the existing single override file, kobo_extra.css.
For example, by taking advantage of the "special Kobo <div>s" which have traditionally been injected during the on-the-fly epub --> kepub transformation:
Code:
/* Put all your epub-specific CSS rules first */
div#book-columns > div#book-inner {
/* Put all your kepub-specific CSS rules here */
}
The epub will ignore the rules in the bottom half because it doesn't contain the special Kobo <div>s . The kepub won't ignore the rules in the top half but the bottom half rules come later in the CSS file so can override the rules in the top half if they conflict.
How well it works may depend on what kind of CSS differences you want for epub vs. kepub.