My first instinct is no, the order of annotations should not matter to a parser. Or, put more precisely: that would be outside the scope of the spec, and keeping track of annotation order shouldn't be required of a valid parser. (Though, of course, if an application wanted to keep these annotations ordered it should be allowed to do so.)

Though it's a great question, and I could see myself changing course if a good use case were pitched whereby the ordering of annotations mattered specifically in a way that a use-case-specific app couldn't function if those children weren't already ordered for it in the plaintext.

There's also a case to be made that, because annotations are just a special type of child items, and because item order is generally meaningful in Margin, then we might as well keep annotations ordered too for good measure.