<< The top part of the door juts out and doesn't sit flush with the car body, and the door midway point slightly catches on the car body when opened or closed. >>

That definitely suggests something has distorted the bodyshell or the door. Gaps on modern cars aren't usually noticeably 'wrong'.

Perhaps someone has tried to force the door open at some point. It could have been worse than this and then the door has been bent back enough to look reasonably ok.

Water ingress will be blocked scuttle drains. Very, very common on these. The under floor storage areas can fill entirely with water.

You need to remove the plastic cover and wiper blades then each side wiper motor. You'll then see a load of water and need to unblock the drain holes. When you do you'll probably have a big whoosh of water and loads will drain out.

It's basically standard on them.

I did read about this, but unfortunately it's not clogged scuttle drains, though they could be causing lighter rain water heard coming into the dash.

There is a persistent heavy sound of rainwater into the drivers door, and separately near the rear passenger door, but I believe the latter may be due to the bent door which is allowing water to run under the passenger underfloor storage box, and also into the mid section of the car.

The underfloor box itself can't be removed easily, but putting anything through the hole on it's edge and down into the car floor comes out soaking wet.

The drivers door water issue has destroyed the door's foot courtesy light. It's a rusted mess.

I've posted elsewhere about all the problems and the car's MOT issues (not mentioned here)
I'm think I have to reject the car back to the dealer. I doubt he's going to cough up for all this stuff and it'll cost me. I guess I needed to see it all in written text, along with replies to get my head clearer on what to do (if that makes sense)

Thank you though.

Doors are designed to allow water to run through them and flow out of drain holes. These are probably blocked and just need a prod with a cocktai stick. However if all these are faults in a car you have recently bought you don't need to get prices to reject the car. These are a range of issues, some trivial, some probably not. You should look at rejecting the car. Bear in mind though that it's one thing having the right to reject and another getting a small dealer to take a car back for refund. Many small dealers are reputable but reputable dealers don't sell cars with multiple issues.

Thanks. My post isn't needed now though :-(
I've been waiting on an independent engineers report, which has now been emailed to me. It summarises at it's end:

"The vehicle was sold with defects that render the vehicle unfit for purpose, and it should not have passed an MOT in its current state.

The vehicle was not durable or safe when it was sold"

Yes, the dealer may decide to break laws even further by denying me my legal rights. I'm well within the 30 days for rejection, but time will tell.