So far so good I hope you choose a paint scheme that lives up to the rest of the job. Something tells me you got it all under ya. 
I don't understand the handle bar choice as I still don't get the high bar on the bagger theme but that's just me.
If you notice where my arms and hands fall on these handlebars, they aren't really high for me. My hands are well below my shoulders. On the stock handlebars, the center rise is low and works it's way up to an elevation about the same location as where my hands are positioned. However, the pullback on the handlebars in the pictures is no where near as severe as the stock bars. As such, my wrists are not crammed and I won't get numb hands.
The handlebars will be painted and I believe the holes in the support brackets will follow some of the paint theme. It's also an opportunity to deviate from the stock appearance. As any custom bike builder will tell you "Stock SUCKS!" .. As you can probably tell, we have attempted to deviate from stock quite a bit on this project.
Finally - everyone has their own sense of design and their own taste. Sounds like your taste would drive you to immediately replace the handlebars - which is okay..

PS: Regarding the paint, yup we know what we're going to do with the paint design. Again, I imagine some will find it extremely cool and deviating from convention (even for custom builds) and others will look at the design and say "Not for me.".
I will tell you three(3) things
you won't see in the design/paintwork.
1. Skulls
2. Flames, in the traditional sense at least
3. Dual Color, upper/lower half, light/dark with tribal patterns transitioning between the halves.