Prefinished is faster, doesn't smell so much during the installation and some people say that the factory finishes are harder. Engineered floors, however, can only take so much refinishing. I like regular hardwood.

Engineered holds up better.

We find pre-finished hardwood on plywood to be the best way to go for anyone looking to stay for the long haul.

The only upside of engineered hardwood veneer vs. solid plank is the factory bond between the solid and the plywood. Properly installed (glued and screwed to plywood) however, a solid plank floor provides the same bond between solid and plywood as the engineered, but you get about twice the sand-able thickness and more than twice the plywood backer for a MUCH more solid floor that will probably outlast your ownership regardless your current plans.

If it is a large floor area, the replacement cost (the labor drive costs) can be substantial down the road. If it is a small floor area that won't cost much to replace in a few years, then the engineered becomes more cost effective (but don't glue it for easier removal later).

We prefer pre-finished for typical jobs due to the variation of finish quality among installers. Higher end custom jobs willing to pay for high quality finishers will be a nicer more durable finish, though.

If you can afford solid plank on plywood glued and screwed and plan to be there forever, in our opinion it's the better choice.

BTW: that is a LOT of house to design on your own. Are you sure you want to rely on a builder and a bunch of suppliers, your own experience and bunch of free advice on the internet for your home's decisions? I'd highly recommend hiring an Architect for at least some ongoing consultation on an hourly basis.