ok but let's distinguish smart things that were done to workaround past blunders
from smart things that you would have done anyways.
Both are "craft", but only the latter is "necessary" and would thus survive the "total rewrite" posited in this "thought experiment".
For example, the x86 is fully of crap; layer upon layer of smarts have been added to deal with design flaws that it was impossible to fix without breaking backward compatibility.
Backward compatibility was practically important, because of network effect (and indeed competitors lose the battle because they were not compatible with x86, or even with their past selves). This practical constrain caused smart people to build smart tricks on top of that foundation.
Sure, it required a lot of smarts to do etc etc but how'd you call it when you end up tunnelling a SCSI command inside an ATA packet wrapped in another SCSI command?