I don't think it is 'by design' it is more just a limitation of the way Archicad elements were created.
SEOs didn't exist until version 8 but by then of course we already had the wall tool, beam tool, slab tool, roof tool, etc.
The way it worked (and still does for the old tools) is the 2D view you see in plan is not a top view projection of the 3D model.
It is all just a symbolic view of the element to the extents that you place it in plan.
Gradually though new tools have been created shell and morph) and the roof tool has been updated to a multi-plane roof tool.
These new tools do show a true 3D top view in the plan so any connections or SEOs using these tools will show correctly in plan.
Eventually the same might happen for the other tools but I think a lot would have to change in the way the program is written.
If you are a relatively new user to Archicad it probably doesn't make a lot of sense but effectively we are using the same base program from 25-30 years ago (which sounds bad I know but I'm sure it has changed an awful lot in those years).
This allows us to be compatible with old jobs - not so much from 30 years ago but I can easily open a file from 10 years ago and still use it.
I am sure Graphisoft could come up with a completely new program if they had the resources but then we would possibly lose the compatibility with what we have now.
Things are changing slowly and I'm sure they will continue to do so in the future.
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