Am I right in understanding that you think you don’t need bridge/tunnel tags, coupled with layer=*, when you see it’s already rendered ‘right’ on the map? That is a backwards assumption. The map should never be leading. If it’s one massive overpass, tag it as such, with appropriate bridge and layer tags.

That it currently shows up the way it does, in the absence of layer tags, is not an indication that it was tagged correctly. It just shows that the current drawing order in the stylesheet for mapnik makes it work out that way, but that may well change in the future, and you do need layer=* to indicate canonically which is the overpass and which way goes under that.