In my experience this mapping style is somewhat common, even though it is of course not a perfect depiction of reality. (In reality, the service area doesn’t extend to the center of the road, only to its edge.)
A reason for this abstraction is that sharing nodes between the service area and the road connects the two features for routing purposes. If the service area was mapped with its real outline, this would then require drawing short connecting ways (which would also be somewhat fictional).
There is no truly clean way to solve this except in a hypothetical future where the road has a polygon representation in addition to the way.
And to avoid any misunderstandings, the above only refers to the specific situation regarding highway ways sharing nodes with the outline of highway areas. In other situations, such as an area sharing nodes with a barrier=fence way, overlapping ways are perfectly fine without any caveat. Most mappers would not consider it an improvement to replace such an area with a multipolygon relation – that would be semantically equivalent but more complex.
Have removed these area=yes problems from the list and as a result I got ~6072 very likely tagging issues (either overlapping ways or missing turn restrictions)
Maybe the community has interests in these I can run this for the planet (currently only Germany).