As a sort of educated guess I think the cockpits needed to be high up to allow room below for a front turret and access for the bomb aimer.
As for the glasshouse, when the Manchester, Halifax and Stirling were designed in 1937, it wasn’t known they were going to be night bombers. It wasn’t until daylight raids were decimated in the early years of the war that Bomber Command switched to night bombing.

Edit. I don’t know about just behind the pilot’s seat, but presumably there’s a step or raised area at the back of the Lancaster cockpit to reach the astrodome.