As the article states, there are two distinct types of underground rail in London: the older sub-surface lines, and the newer tunnels. The coal trains were never used in the tunnels.
I don't think I get your point. Presumably ventilation is easier to engineer near the surface, but air quality is always going to be bad if oil/coal/coke/smokeless coal are burnt (or are you saying that these fuels weren't used, which would be incorrect).
The claim is that the air in the cut-and-cover lines would be no worse than around a surface coal-burning train. Which could still be pretty bad, though probably not uncomfortably hot.
I'm not sure what the difference is between the two. Aren't they both underground?
Here's a video of a steam train going thru the underground to celebrate 150 years of the tube:
https://www.youtube.com/watch?v=a3_rxuOFTm8
The sub-surface lines were built by digging trenches and then covering parts of them back up with roads, buildings, etc. This technique is called cut and cover. They're just beneath the surface and large stretches of them are actually open to the air, many were built for coal powered trains. These can be built without tunnelling. They're below-ground but not usually "under ground". The trains are rectangular shapes since that is the traditional shape for a train.
The deep lines (originally called "the tube" although that now refers to the whole system) were built by tunnelling, the trains and tunnels are cylindrical and the trains just fit into them. In many cases the tunnels are 30+ metres underground.
There are differences in loading gauge (things like maximum train height)--you can't run the subsurface trains on the deep tunnels because they're too big. Also, like many subway systems, there's a mixture of surface and underground sections (surface segments primarily on outskirts).
