Don't know about dot, but those smudges are definitely "tool marks". I have one on my SSFG downstem, that is slowly wearing off. Simple Green helped some, but then I was able to rub it to.
That dark and location... I wouldn't want to guess. Glass guy really needs to make that call. Certainly worthy of emailing concern and if it fades as slower than mine... I would want a replacement to.
EDIT: Then again, yours looks more granular and possibly easier to come off. Mine was actually made worse, when I received it. I saw a little tiny black mark and just went to rub it off, whoops! 1" long smudge now. The glass cleaning stuff, might work. You might want to try something like Formula 420, which is the blue granular shit. Works well, on open pieces like that.
Also, the more I look at that "dot" in your full-size pic... I'm thinking its the same stuff (not in the glass itself). Same color and consistency (taking the lighting into account). In fact, the lighting looks like its reflecting off the top of it. I don't think it would be that highlighted, if it were inside the glass. But, then again. I'm not holding it.
EDIT II:
Larger 2 circles, graphite "tool marks". Smaller circle, looks like tiny bubble.