You don't really have to "make roads transparent" - usually you should tag to the best you can, and leave the displaying to the renderers. You might have heard "do "[do not tag for the renderer" renderer][1]" suggestion :)
The idea is that it's best to tag things as they are. There are various renderers and styles, and it is up to them to get things right/beautiful.
In this case, though, you could make the roundabout and connected trunk_link ways all trunk, or make those two secondary attachments secondary_link. With the default renderer, it would draw trunk segments on top of the secondary segments.segments.
[1]: https://wiki.openstreetmap.org/wiki/Tagging_for_the_renderer