It appears the pitch was flattened from the original plan? This makes the serrated gables look off and results in a very challenging standing seam detail. The panel rib spacing won't line up with the awkward valleys that come to points at the eave. Yes bad workmanship but design seems to deserve much of the blame. Other than sticking to original roof plan or improving dormer design I think the move would have been perfecting the valley intersections first and accepting less than ideal panel rib alignment.

You could do any combination of what is suggested above. Painting all one, lighter tone would give the most contemporary feel. However, be careful to make sure whatever you do in the house is consistent throughout. For example, are those beams and corbels repeated in other rooms? Also, if you leave the ceiling and/or beams darker, I would definitely get a round rug in there. Right now, the ceiling feels very weighty over the table. A rust-colored rug to mirror the ceiling would be great. I would change out the chandelier for something simpler. I'd like to see something that mimics the beam pattern. Finally, keep in mind that this is beautiful and unique. I would think long and hard before I'd paint the beams.

Yes to the obscure glass or even heavily patterned glass like rain glass. Would you consider painting it red? Not a bright red but a subdued darker color red. That might coordinate with the other chest in the photo above. I do like that it is a stackable piece. Would be great for a home office. Not sure what to do with the accompanying box though. That could be decoratively painted and used elsewhere. Good luck!

IME, flat roofs are prone to leaks and getting ripped off in high winds. If you decide to keep repairing your flat roof, look for the best roofers you can get. It may be possible to rebuild as a Dutch Colonial style without removing the existing trusses. Consult an architect and a contractor if you are interested in that route. https://www.houzz.com/magazine/roots-of-style-dutch-colonial-homes-settle-on-the-gambrel-roof-stsetivw-vs~16982070