A continous run ridgevent is best when used in conjunction with continous run soffit/eave venting. The air is drawn up through the soffit/eaves uninterrupted up and out the ridgeventing. Any existing venting such as gable vents would need to be blocked off. Ridgeventing alone would be better than the box vents, imo as with a cape, you might not have existing overhangs for soffit/eave venting. If you have a small overhang on your cape, typically about 6", it could easily be made into a continous run soffit venting. I always recommend tearing off the existing roofing on older homes as it gives you the oppurtunity to see the conditions of the roof sheathing for any rotted areas, inspections of all flashings as well as any roof protrusions such as plumbing vents. I can't speak for Atlas, but here's a link and Im sure there are others that you could look into concerning shingle ratings. Here is a link that might be useful: shingle ratings

OMG! Brazilian peppers are banned in FL if I'm not mistaken. If/when you remove those, be VERY careful to get all the seeds. Those are carried into the wetlands by birds and, well, there's a good reason they're banned. We need to ban them here, too. Mangos are simply a pain in the butt. Nobody can eat the fruit fast enough because they all ripen and fall off the tree on the same day. You go from a clean yard to literally tons of fruit on the ground overnight. Banyan trees look nice as a gigantic ornamental specimen in an even more gigantic open space. You don't have that. That's the wrong tree in the wrong place. So I guess I'm saying you need to get rid of all those trees. All of them are the wrong tree in the wrong place. The palms can stay - maybe. At 30 feet high it's not like you can enjoy the foliage. They are simply a big trunk you have to mow around. At least they are not a pest and won't interfere with grass. Okay so currently the only grass that even might survive is St Augustine, but I would focus on tree removal before spending another dime on the lawn. Any grass you install now would get torn up with tree removal. Plus if you get rid of all that shade your choices of turfgrass open up beyond just St Augustine.

Table 402.1.2 from IECC 2015 to current is best prescriptive guideline for cost effective energy efficiency. I doubt using weaker local amendments is good strategy. Some energy efficiency experts feel that R49 is good minimum for ceilings in ALL climates and would agree, if the ceiling is traditional vented attic where thick layers of insulation are easy to apply and affordable (loose fill). Some high performance projects in cold climates approach R100 for ceiling. These are international code minimum prescriptive numbers and it's easy to use other compliance paths to demonstrate equal total performance through other balancing improvements. Renovations of vaulted ceilings and insulative sheathing above the roof deck can make sense to go with weaker values. Spray foam applied to bottom of roof decks usually have substantial thermal bridging through rafters or truss chords, often more than the vented attics that prescriptions are based on so I don't think they deserve much leeway. Martin Holladay has the classic article on this common code violation. Efficient homes heating with mini-splits don't need heads in every room, but will need their doors open during hot or cold weather, a deal breaker for many. Then there is David's point about resale but I think good implementation could help tamp down this possible sentiment. Haven't built ductless yet but open to it if owners are. The efficiency one gets with Mitsubishi's smallest unit is unbelievable. One head replaced a whole house furnace in my personal small home, granted winter design temps are stretching it. Energy Star is for all homes. Homeowners or owner builders are eligible but may have a steeper learning curve to get the right details. Always involve a rater early, preferably with feedback during the design stage. Cpartist, sorry for your trouble. With everything you have had to put up with, it's not surprising they flubbed an important technical detail of your build. I think people who value efficiency have to do extra research to ensure they are getting the right feedback on their design and selections. The architect or builder should have the right knowledge and experience in your goals and I think the best projects are collaborative from the beginning. Most build teams valuing efficiency still include HERS raters (Energy Star) and mechanical engineers specializing in HVAC for services like Manual J, D, and S. Third party diagnostics, commissioning, and verification usually help ensure a good investment in home performance certifications like Energy Star.

A question first- is this a shed roof so the furthest edge of the roofline is the highest point, or is there a gable? All wood changes color with time as the wood and the finish age. To some extent the interior and exterior will never look the same- the lighting is drastically different and they will be viewed through uv glass.