Depends on the train-to-tunnel area ratio surely? If it's a close fit like the London underground you'll get a lot more drag on a train at 100k feet than you would on a plan at 100k feet.
Commercial aircraft fly at ~30,000 feet which is ~30% atm vs ~1% atm at 100,000 feet. That’s edge of space territory, but sill a long way from LHC style vacuums.
PS: In terms of force it makes little difference as you go to ever lower fractions, but it’s much harder to maintain and pump down the pressure as you keep going lower.
I think they were referring to the fact the air has to move out of the way, and in a tunnel there's less space for the air to move to, thus the drag is higher especially if the cross section of the vehicle is near the cross section of the tunnel.
It’s something to consider, but you need actual numbers to do so. Are we taking 1/3 Atmospheric pressure and 3 inches of clearance vs 1/300th atmospheric pressure and 3 feet of clearance.
Really, nobody is going to build a system where this is a significant issue past the design stage. So, IMO it’s a consideration but a non issue.