I know you will hate me for this, but please understand my view point. I am an old house LOVER! I also spent twenty years as a banker trying to talk people into understanding that their future home purchase had to be about love....and practicality. When you are in love with a house you think that the fact that it slapped around the last owners was likely because they were bad owners...they probably deserved it because they didn't do the maintenance you would do to keep it in check. You justify the little issues like the third eye as something minor instead of realizing that a third eye is not actually a normal thing and will require some seriously expensive custom lenses. You turn a wet basement into a couple puddles.... Ten years,..no lets make it five if you get the house....if you find that my pessimistic attitude was totally incorrect and your home turned out to be perfect beyond compare...please tell me I am wrong so I can learn a lesson. But if on the other hand my gazillion years of trying to make people understand that they should buy a home they love....but should equally involve their brains and heart in the equation turns out to make some sense in your potential chris brown like situation.....well be sure to share that valuable experience as well so that others can learn from you...and make light of your experience because "that will never happen to them". I tried to buy the egg and I farm as a young wife ohhhhh so many years ago thinking that a house with walls falling down and a tree growing in the living room just needed our tender and inexperienced care to bring it back.....the bank laughed...thank god!

One idea, since the room seems large enough, might be to plan your room with the objective of turning the bed so the foot of your bed is closer to the windows than the head of the bed -- you'd face the windows as you wake up. https://www.homedit.com/5-diy-practical-headboards/bed-with-headboard-storage-behind/

I am not a pro, not a pro, not a pro. But, I like the bench, and think it's functional for exactly the reason you stated first--you need a place to set stuff. I like your chippy paint ideas. try it! If it's not your favorite, you can paint over it. I like the idea of hooks above the bench, as well. But I'd put them in the far corner, so no one hits their head on them while they're making the bed.

You might look at doing a bench at the end of the bed and then placing two chairs on the blank wall in photo number 3. It might be smart to angle the chairs and place a small side table in between and you can do a small rug under them as well. See some of our bedrooms designs for ideas: