Couple of pics would help. As for " keep the smaller window, frost it and have the builder remove the inside trim then completely drywall over the window keeping the look of the window outside but losing it inside? Will it look half ass and dickie?" Yes.

I agree with havingfun, thicken the supports and have something growing trailing up them. I didn't even notice there was a pergola until the close up. Right now it blends in too well with the house color, consider painting it a different color. I don't know your usda zone but classic climbers for a pergola include clematis, wisteria, grape https://www.houzz.com/photos/santa-ynez-valley-mediterranean-porch-santa-barbara-phvw-vp~2485412 or go for a modern look You can also hang string lights, planters or something from the beams. Also agree lighten the front door.

A very simple layout keeping the floor space within the kitchen, the WIP takes up a lot of space with not much gain, The broom cupboard could be moved to the Laundry/entrance, narrow. If the wall has been bumped out to the eaves on the deck side giving an extra 300 depth to the kitchen you could make the island 2700 x 1200 and all drawers. The wall of narrow pantry will hold all pantry needs and more, no deep cupboards to dig into. cheers

These spaces can look awkward but yours is quite inviting with those windows. It could become a retreat space, that allows someone to be near the action without being in it. Seating or lounging would work with the very low head height. I could imagine it would be a great spot for a couple of cool beanbag seats, a small funky bookshelf and a sleek retro lamp, or if you have children to cater for a games setup with storage in a retro ottoman.