Oops I forgot to link the screenshot. Here it is:
https://imgur.com/UwvsTbn

I’ve drawn an outline around the problematic part of the Western Distributor. Note how the orange motorway lines are hidden underneath the beige bridge outline. In real life they physically sit on the bridge though (unless I’m getting mixed up - also possible 😆). 

> I believe roads *always* draw over the top of closed ways/multipolygons, which would ultimately be for clarity I would assume.

Yep, that does seem to be what Carto does (the default osm.org renderer). Carto is just one of many renderers though, and in this case it seems to be hiding a problem with the layer tags. 

If we set the layers correctly here, then:
* Nothing would change in Carto, as it always draws roads on top of bridges anyway. 
* Renderers that do consider bridge layers (such as Organic Maps) would display things correctly. 

Fixing it might be easier said than done though - as you say there’s a lot going on in this area! I might have a go on the weekend if I get time. 