New 24G Standing Seam Install

As far as the chimney flashing, from what I can see, it doesn't look bad. As far as the valley, most folks would call for a cleated valley for standing seam. I would recommend going back to the manufacturer of the standing seam for their recommendation. A cleated valley would have cleats that the metal panel ends are folded and locked over.

It's actually pretty common with chimneys on standing seam roofs, especially the downhill side (where the panels slope away from the masonry), for the flashing to come out over the ribs. I saw the one photo you sent and, while that method looked great, it's actually pretty uncommon. Typically in a situation like yours, a Z Cleat is used between the panel ribs and sealed and the chimney flashing locks over it. The uphill side is of course tricky and done differently. The sides also usually have the flashing on top of the panels but a lot depends upon where the ribs fall.