Totally, and this seems to be exactly the type of tunnel that the article’s author is discussing, evidenced by the second point they make:

> Tunnels have a smaller height difference than bridges. Only need clearance for the height of a cyclist, not for trucks or trains plus electric lines.

I think they meant tunnels in general that affect people not in cars, including motorcyclists, because of their lack of a loosely airtight or climate-controlled environment. As opposed to a tunnel specifically for bicyclists and motorcyclists, which is also how I read it at first.

The Kennedytunnel in Antwerp is two-level with a bike tunnel on top of the (very crowded) motorway, and it does smell of fumes in spite of the ventilation.

The large detours of the bike path at both ends of the tunnel are also a bit annoying as they significantly increase the distance you have to cycle. The alternative with elevators like in the Sint Annatunnel isn't really better though, because there you just have to wait for a long time for the elevator.

I much prefer bridges but where I've used bike bridges (like in Nantes) they were very low with little clearance above water. Even in Lille they're just a few meters, maybe ten meters at most, above water, so they're easy to climb without a large detour.

I wouldn't take the Pont de Cheviré on a bike for example...

I immediately thought of the Rotherhithe tunnel in London. While pedestrians and cyclists can use it, it's grim - see this video for example of someone walking it https://www.youtube.com/watch?v=hjAHzZa_pc8

Clearly for crossing any lengthy stretch of water, a bridge is much preferable to a tunnel.