So, only reason for this tagging - for renders. https://wiki.openstreetmap.org/wiki/Tagging_for_the_renderer

Good practice - tunnel=building_passage without any layer: 

https://wiki.openstreetmap.org/wiki/Tag:tunnel%3Dbuilding_passage
"The layer should be the same as the layer of the building, with the exception when several tunnels are passing on different levels. So if the building doesn't have a layer tag, the way should not have one either."

Also, that's about using layer for buildings. Yes, layer is not level. But building and zero floor tunnel has same layer.
