That’s a short-coming of DT’s MD interpretation, afaik. And it is not about “relative” vs. “absolute” references (media/something.png would work if media were a group below the one containing the MD document) but about “parent” references (../).
Which makes kind of sense, I think. Imagine you have a MD file in your global inbox – what would ‘…/foo.png’ refer to? There is no parent element to the global inbox. That’s different from the file system, where /../ is the same as /. DT’s hierarchy of groups sometimes looks like a file system, but it isn’t one.
So you just have to stick with what DT provides. I’d suggest putting MD documents and the images they refer to into the same group.