I have a little of that on my boat, enough to know exactly what it is...
The black marks are just tarnished aluminum where the Shark Hyde either didn't get applied, or it got rubbed off. Looks like some of each to me. That's why he was able to scratch the "E" into one of the spots. He just scraped off the tarnished part. Guessing there's a permanently scratched "E" in that tube now.
As long as there are no dents, I wouldn't be afraid of this, but you will need to buff and polish these spots out, then reapply the Sharkhide over them again.
I've only polished and Sharkhided once. I've not gone back to fix these little spots (on mine, they are very small) so I do not know how it would look once Sharkhide is reapplied over those parts.
Think of Sharkhide as a clear paint. That's what it feels like, and once you polish aluminum, and put on the "paint" (Sharkhide) it seals up the aluminum from water and air and keeps it from tarnishing. It's like a plastic top coat. Or clearcoat, like on cars.
Polishing an entire pontoon is very labor intensive. Fixing spots like this wouldn't take a lot of time, if you have the stuff to do it (polisher, rouge, rouge rake, etc). Even the "E" should be able to be buffed out.
Again, I wouldn't be afraid of this boat just because of those spots. I'd be MUCH more afraid of dents. The black marks can be fixed. Search on Youtube for aluminum polishing, then judge for yourself if you think this is something you can do yourself.
BUT, I would never buy a boat without being able to touch it and test drive it. You are putting MUCH faith in this dealer.