> It leads with considering "unit" to be "the whole system" being bad
I do not understand this statement. Could you point out which part of the article you mean.
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> when people started considering the system under test as the “unit”, it significantly affected the quality of test suites (in a bad way)
It should be "when people started considering parts of the system under test as the “units”"
Units are parts of the system. Perhaps you want to say something about granularity?
The claim in that phrase of the article is that a "unit test" was originally supposed to mean "a test that runs unitarily, by itself". Conversely, the more common interpretation of the term is "a test for a single unit of code".
So, according to that phrase, units are not part of the system. The units are supposed to be the tests.
Note that I don't agree with this semantics game. But that is the intended meaning of that phrase.