1). Supergirl counter zones Superman, that is true.
2). Superman can interrupt the gaps into breath just fine, I literally tested it in practice before writing this, it's incredibly simple and I don't even play Superman or practice interrupting Supergirl's gaps and I can manage it easily.
3). Superman has just as many ways to open up players as Supergirl, he wouldn't be top tier material just like Supergirl if he didn't.
This is not a "true uphill battle." It's even.