Think this is a classic example of step-mum's getting a kicking on MN. I think some of the replies have been really vile.
Reading all OP's updates it sounds like her OH thinks EOW will keep on as is and she's worried he's wrong.
OP I think he might start coming less regularly, especially as all his mates are in Manchester and you're a long way away. BUT I think if he's close to his dad he might start coming for longer chunks when he does come. Which may well last into adulthood. So maybe a week in Christmas break. A week in the summer and so on. He's also at an age where he might want to bring girl/boyfriends back.
You might also want to consider that if he goes to Uni then Manchester may well end up not being where his mates live. So the pull of his mum's decreases and he spends more time with you.
For those reasons I think the dining room situation won't work well due to 1) comfort and 2) privacy. And so his contact might deteriorate quicker and faster, which I presume would upset you and DH.
Someone suggested a garden annexe type situation which would work brilliantly if you can afford it.
Alternatively you could turn the dining room into a permanent guest room which is "his" but doubles up for other guests. Or a bedroom / office that again is his but can be used when he's not there.
Alternatively - as PP's have suggested if you're dead set on the youngest having their own rooms generally then you could just move them to share when he comes to stay (this might be tricky with bed sizes tho).
I do agree with several upthread who've said littl'uns like to share, so I do think putting your youngest together for the next five years or so is a good option.
Then the other bedroom can be his / guest generally which will help if friends and family come. Can be re-evaluated when they're seven / eight and he's through uni and an adult etc.