The special issue certainly wasn't a matter of joking around, but it also wasn't a normal issue of the journal. After he submitted it they wrote to him (wikipedia quotes them): "We requested him (a) to excise a good deal of the philosophical speculation and (b) to excise most of his footnotes."
They stuck it in the special issue after he refused to make these changes.
It doesn't matter what issue they put his nonsense in. What matters is that his article was designed on purpose to look 'intellectual' but was made up of total nonsense to prove his point that the editors will allow any junk to be published as long as it looks 'sophisticated'. And he indeed proved it. That's it. They would be better off just admitting that they made a mistake but noo, instead they pretend that nothing happened and it is all just a misunderstanding. And you completely unnecessary carry water for them.
They stuck it in the special issue after he refused to make these changes.