If you want an in-world answer, then the sixth chair (there are usually six) was made to be not available due to as-yet-undisclosed circumstances. The extra place setting is there because some of them don't hate R.
Otherwise, well, that layout works best for that shot. The extra chair is there to push Morty off to one side of the window, and it's missing from the front side to keep the scene open, with Summer pushed over for balance and the floor detail to... do exactly what it is, and help explain her location.
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