I did some quick testing with my low-fishing-level shaman on the PTR this morning, and can safely say that at this point in testing, you can get skill-ups fishing up the new grey junk items. I stupidly quit out forgetting to take a screenshot, but I took thirty casts in the sewers with the corroded jewelry quest, and am fairly certain you cannot fish up quest items with junk.
The rate of skill-ups appears--at least at low skill levels--to be the same as catching non-greys, as I went from 72 skill to 101 in thirty-four casts.
But now for a real question: how exactly did driftwood get into the Eventide fountain?