From a modelling perspective, the Commanders popping out of the cupola could be for more stationary dioramas, with the Commander issuing orders not only to his own vehicle, but to the surrounding regiments and units. I think this also makes sense in gameplay, as iirc Orders are measured from a vehicles hull, rather than a specific entry point or cupola.
You also have to take into consideration that all GW miniatures are Heroic scale, meaning that almost nothing is in scale to anything else (Guard being the same height or taller than a Space Marine depending on modelling, for example). Looking at real world cutaways of tank crew positioning, it seems that the turret can sometimes seat two people, meaning a Chimera turret could have one person (the commander) standing up and out issuing orders, while a second guardsman handles the loading and firing. This does assume that 40k tanks have some sort of autoloader system, which could be argued as cannon, due to vehicles (Mainly tanks) having a Machine Spirit, which we would consider as an automatic system.
For both Chimeras and Leman Russ tanks, the Driver and forward gunner would most likely be side by side, though with the gunner sat back slightly to account for the gun and targeting mechanisms.
Sponsons can be a likely tricky, as tanks often have increadibly chunky wheels to support and guide their tracks. A sponson gunner position would either be increadibly cramped between these wheels, or more likely considering the apparant bulkyness of LeRus the Sponson gunners occupy an area beneath the turret gunner positions with some sort of targeting mechanism (which would explain the "Cameras" on sponson turrets).
Thats just my thoughts on the subject at least. I look forward to this Novel, especially if you'd post some choice cuts from it to the forum