That is indeed the same color I mentioned; brownish color:
Rasterize[Style[Quantity[14, "Electronvolts"], 100]] // ImageData // Flatten[#, 1] & // Tally // SortBy[Last] // Part[#, -2, 1] &
As said before, if you look at my example, you would not be able to see what is what. (only if you happened to hover over it, which I just discovered because you mentioned). That said, a visual clue is very nice. I like it very much.
What you call an issue, i would call a very useful feature. If you want to put it in your paper you can use something like:
ToString[Quantity[14, "Electronvolts"]]
ToString[Quantity[14, "Electronvolts"], TraditionalForm]
to make it in to a string that you can style the way you want using Style.