When you say fudged up eave and transom do you mean the roofline not being symetrical to each other and the transom (assuming arched window) being centered down the middle? If it's a look thing I really don't care. The framer has been in the business for decades and might switch it up on the fly if he doesn't like it.
And I have no idea what a prime corner is or why I would be concerned about what's placed there.
We're cool with the MB placement. It's close to the door to take the dog out at nights/mornings and 99% of the rest of the traffic will go through the garage entry. The door is almost always closed to keep the dog off the bed
We wanted it away from the main living space so it wasn't loud in the morning when somebody is making breakfast or watching TV in the mornings if the other wanted to sleep in.
it's kind of a look thing, kind of a "just doing it right" thing. What your builder has done is mishmashed various historical styles and cut some corners along the way. Doing the eaves like that is quicker to build, but it's wrong - it doesn't match any of the historical styles being loosely referenced in the rest of the house. As a result the whole roof looks kludgey, or off.
Transom/window details are a similar story. They picked window arrangement and proportions from a mfg catalog without even trying to get it to match with the neocolonial /federal style the house more or less seems to be referencing. Neocolonial houses only have arched transoms in certain situations. Same goes for paired double hungs - fairly rare.
Floorplan wise, this is a house plan for a densely packed subdivision. I know that because there are no windows on either side of the house, and utility spaces (closets, bathrooms, garages) are pushed to those sides, insulating your public living spaces from your neighbors.
But from your pictures, you don't live in a densely packed subdivision. You have views from the sides and corners of your house. But you can't make use of them because you've got a closet and a garage taking up the best space.
Now if you tell me that the house faces East, that's really gonna be a facepalm.