A possible explanation for the whole "new decal for the name but not the registry number" thing. I remember buying press-on letters to make decals myself, and the sheets they came on usually featured letters or numbers, but not both. So the purchasing guy says to himself: "Well we need a new name, so we'll definately need letters, but I won't buy a numbers set too, we can just rearrange the numbers we got."
That's the most sensible explanation I've ever heard.
This is the oft-repeated explanation I have been given, together with the fact that the fontface was commercially avaliable as dry-rub transfers in the 1960's. To my knowledge, the effects company built the model, and Jeffries had nothing to do with it.
My personal view is that the Constellation's low registry is explained by the number being reused in memory of an earlier Constellation that was lost in the line of duty. The use of the lettered distinctive for commemoratively named ships didn't begin until the Enterprise. (Of course, in my universe, the Enterprise would still be NCC-1701 regardless.)