The general idea you're missing here is that it's very hard -- perhaps impossible -- to develop a clear, bright-line method for distinguishing between fields that deal with concepts we can't empirically test, in such a way that it will put mathematics into the "good, useful, keep doing it" side and metaphysics into the "bad, silly, stop doing it" side.

And in fact mathematics is a great place to dive in, because one very important question -- namely, whether mathematical realism is true¹ -- is really a metaphysical question, and one which can never be answered by empirical observations about the world.

I'd also caution against too much scorn on philosophers going "beyond the reaches of their knowledge base"; historically, philosophy's successes have spun off into entire fields whose origins we now like to forget or at least overlook.

(and, well, I've had a successful career in programming, and also hold a degree in philosophy, and I think the basic observation that lots of people do metaphysics who we don't normally think of as doing metaphysics is a sound one, regardless of how you feel about the paper's specific examples)

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¹"Mathematical realism" asserts that truths of mathematics are necessary and discovered, rather than contingent and created, and thus have some sort of existence independently of human minds and human culture. The exact sense in which these mathematical truth-entities would exist is, of course, a metaphysical question, as is the question of what mathematics really is, if mathematical realism is false.