These licenses are often encumbered with legal restrictions because the creators (via their agents) can get more money by subdividing the rights.
This isn't specific to music. I can speak from personal experience about novels.
A common form of encumbrance is territorial rights; for example, when I sell the rights to publish my novels to my publishers, I only sell them the right to publish in a specific language, and in specified territories.
I can't get more money from a publisher by offering them world English language rights rather than, by splitting US/Canadian and UK/rest of world rights and selling them to different local publishers. (In fact, if I sell world rights to a US publisher, they won't sell the ebooks around the world -- they'll merely re-sell UK rights to a British publisher, who will maintain the territorial split. Because there are still no truly global publishers, despite individual members of the Big Six trying to operate on a global scale.) So I split the rights and sell them separately.
As noted by, well, just about everyone, this makes little or no sense in the internet age. Unfortunately trying to get book contracts re-drafted so that e-book rights are global and non-exclusive is, shall we say, an exercise in pain (we're talking about getting publishing house lawyers involved: do I need to say any more?). So that's why it persists in ebooks, and it's pretty much the same story with other forms of content.
That's why this goes on. It'll probably continue for a few more years before truly global distributors show up and the existing system collapses under its own weight.