In the original (1861) article (big red link halfway down that page), Figure 2 (the tower reaching above the surface) is described primarily as a ventilator to draw away “smoke and foul air”. He had thought about it.

Atmospheric/pneumatic railways were still a popular idea in the mid 19th century. The Dalkey and Paris – St Germain atmospheric railways had each had over a decade of service before closure in the 20 years before Chalmers’ patent. They obviously had their own, considerable issues, but would have reduced the ventilation requirement.

We simply run the trains backwards, emitting exhaust behind us!

(ofc the trouble is how to handle the next train coming in 15 minutes)

OTOH there are such a thing as 'fireless locomotives' which just load up on steam pressure from a stationary boiler and then operate for some miles without need for fuel or any exhaust more noxious than water vapor. But this scheme didn't come for some decades after 1861. I wonder if a cable car would have been feasible.

They have another article about a more conventional tunnel idea that addresses that issue. They were well aware of the issue. The only way to make this work at that time would have been something like Brunel's atmospheric railway. That was plagued by issues when in the open, goodness knows what it would have been like to run underground for such a long distance.

https://www.theengineer.co.uk/content/in-depth/this-week-in-...