A single vertical flue has rather limited surface area and is not very well heated as there is nothing impeding the hot gases of combustion from doing that which they most naturally do, ie: rise rapidly and exit out the chimney with only minimal brief contact with the part of the flue in contact with the boiler's water. It is usually best to have several small water tubes crossing the vertical flue to slow the heat rising and provide significant increased surface area of heating. In lieu of that, then multiple smaller flues is a good way to increase the heating surface area and is often used.
As for the "Metallic Smell" I would suggest that if it has never been heated before, that might not be unusual. It is also possible that it is assembled with certain dissimilar metals that are not quite at ionic equilibrium with each other, thus heating would instigate or accelerate any galvanic reaction that is "potentially" (pun intended) extant!?!?
If that is the case, then you may well get that smell every time you fire up, though likely less as time goes by. It is unlikely that you will note any significant deterioration in your lifetime, but depending on the metals involved, it is possible!
My concern is that the top part of this single exhaust flue is overheated as the top portion of it isn’t in contact with water. Is there any danger to that?
Your flue is presumably copper or some alloy thereof, so transfers any heat it receives quite readily, I suspect that there is no part of your flue that is more than an inch or two above the boilers normal water level, so I don't think you have much to worry about with overheating the flue itself, unless your water level gets extremely low or you boil dry. Now your chimney has no contact with water and is only a little farther on the path of exhausting heat. If your chimney is surviving without any water to transfer its heat to, then I would suspect that your flue is doing just fine.
Thank you! That’s helpful. I’ll try steaming it a few more times and see if I can still smell it.
It was like a very earthy copper like metallic smell or something like a stink bug and copper. I highly doubt it but maybe there was an insect inside it.
Edit: The chimney doesn’t have pressure associated with it. I just hope the exhaust flue isn’t thin metal, where as the chimney wall is like 1/4” thick.