I wouldn't stress out too much on tension. I never used to worry about it at all, just went by feel and sound of spokes when pinged and built wheels that lasted for years and never needed truing. Finally, I bought a spoke tension gauge, I really use it more when first tensioning the spokes, just get everything sort of even as a baseline and work up from there. By even, I mean +-10%. A lot of this is going to depend on the quality of the rim, getting even spoke tension. Sometimes you are just going to have a tight spoke or two unless you want to possibly discard the rim.... But if you are habitually having a wide range of tensions, maybe you might rethink your wheelbuilding process a little - as i mentioned, I like to get spokes more or less equal tension at a level mayber 20% or so below final tension and then be adding tension via dishing, roundness adjustments, or just going around the whole wheel adding tension to spokes if those dimensions are ok.

As for the nipples, that seems a little high, but the real question is how far below the rim tape surface are these spoke ends. You can get a pretty good idea of how much the rim tape deforms into the holes by looking at used rim tape. If you got a lot of margin there, I wouldn't worry a lot about it, although others may.