I'm almost certain there were more produced in the burgundy color than just a prototype or two. I think there was a choice between that color and the green, but perhaps not in equal numbers. You could probably spend some time on the wayback machine (internet archive) and find out for sure.
As to the lack of creme headtube, it was probably an aspiration that didn't pencil out once the final costs were known. The thing about Rivendell is that they are very open about sharing details as projects and ideas develop. It is fun watching the process and is nice in that you get to plan and anticipate, but can lead to disapointment if you get your heart set on something and become emotionally invested. Details always change.
I'd say paint it as you'd like it. If it's a quality, professional paint job and in a subdued, tasteful color that works with the decal, it's not like the bike is devalued. Same with adding the creme headtube and wings and window fill, if that's what you like.
When the quickbeam (the japan- made predecessor and template for the simple one) was in production, I think there were a couple of one-off versions made, with fancier lugs and/or fancier paint. In fact, Riv used to offer the option of custom paint
on production models, at the buyer's expense and in approved colors.