According to the article, they're moving people to IPP (the protocol CUPS uses), with the difference that it will warn if configured with encryption disabled (I can't be bothered to check to see what CUPS does for transport encryption by default, but according to MS, it does support it out of the box).

Other things they mention are just a function of having access to the source code (CUPS drivers are mostly open source), and not letting people install DLLs with elevated privilege over the the printer network port (as far as I know, this was never a thing that cups supported). They mention XPS (isn't that dead yet? Is it more secure than PDF/A, or PS?) and Mopria (not sure what this is, but the specifications page on their webpage only mentions things that are obvious security holes: piping your print spool through the cloud, and having the device advertise using Bluetooth Low Energy)

Anyway, CUPS has none of the problems mentioned in the article from what I can see. (Except that it might be common practice to misconfigure it with transport security disabled).