An iOS version or so ago, this would not have been possible. With few exceptions apps are sandboxed and can not access information from other apps. That would include the audio stream. Especially a live audio stream.
Now it is merely difficult, or perhaps inconvenient would be a better word.
Apps can now pass sound streams from one to the other, live. However, it has to be built into both the original app and the modifying app, and both (or more) apps have to be running, therefore using up resources. It would only work with apps that included the ability to stream to a second app, or through a third bridging app.
The setup would also be more complicated than including equalizer settings in the app; which is why I expect most music playing apps continue to do this, or nothing at all.
It is my understanding that there are JailBreak tweaks that will do what you want, though I doubt any of them are compatible with iOS 7 yet. You can go to the Hacking area of this forum and read up on Jailbreaking if you like, and keep an eye on if/when the iOS 7 Jailbreak will do what you want. If you are not familiar with Jailbreaking, check out all the sticky threads first. They should answer most of your questions.