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A bit further down in the same article: "Unfortunately, this method did not allow us to intercept HTTPS traffic of Apple services (including iMessage), as iOS implements SSL pinning for this"

It would have allowed them to intercept those bogus malware domains though.

It did.

Without having to redo their setup when their network was not intercepting connections by default, which it could have been doing.

(This is sarcasm, right?)

Only partially. As an employee I would resign from a company that insisted on MitM'ing my connections. But from the position of the article, it clearly would have been valuable to have request captures from the start rather than having to try to reproduce the malware a second time.

Then you have other problems.

The risk of getting your MitM box compromised is too high IMO

Is this risk analysis real? I don't believe in companies that think this is a risk at all if their box is implemented properly. If it's even possible to compromise then you have bigger problems (like your intranet not being properly secured, or the MitM setup not being sandboxed properly, or .....)