Note that they don't care about the themes their end users pick, though. You can theme your app just fine. They just want operating systems using their software (with their logos, trademarks and support links) to stop shipping their custom themes by default.
They just don't want Canonical or Fedora to ship a theme that makes all applications that didn't come bundled look like shit. If you like the Windows 95 Hotdog Stand theme, you can configure that and everybody probably agrees that that's great. If you inflict that pain upon yourself, that's your problem.
The current "solution" to themes breaking applications is to just not follow the system theme any longer. Everything gets packaged with a hardcoded theme in a sandboxed environment and you'll just have to live with that.