I did think about getting it blended in but it was a lot more expensive and I got the impression the body shop wasn't that keen on doing it, given the potential for cracks etc over time. A single piece bootlid with ducktail is available for the earlier mx5s but there is relatively little out there for the newer models sadly... I agree single piece would look loads better.
As for the black roof... I wanted a red one but this black one was available locally and was very cheap. I was gonna get it repainted but it's grown on me, looks like many of the limited edition mk3.5 mx5s which have black mirrors, wheels and folding hard top roof.. Might get the screen surround wrapped gloss black to match, go all the way. I like the car but understand there are those who aren't keen on the changes.