The rumor I've heard is that Apple is keeping their custom extensions to the ISA undocumented in deference to ARM's desire not to have the instruction set just completely fragment into a bunch of mutually incompatible company-specific dialects.
It's worth noting that the article you link predates the public release of the M1 by a good 10 months. Given how secretive Apple tends to be about these sorts of things, one can only assume that it was based almost entirely on rumor and conjecture.
But it's not really about trying to prevent anyone from discovering that these opcodes exist. It's about trying to discourage their widespread use. If it's undocumented, then they don't have to support it, and anyone who's expecting support knows to steer clear. That gives them more freedom to change the behavior of this coprocessor in future iterations of the chip. And people can still get at them, because Apple uses them in system libraries such as the OS X implementation of BLAS.
https://www.eejournal.com/article/whats-inside-apple-silicon...
Can you provide some more information on this? I would love to be able to hit them on this, as this would actually be really upsetting to a lot of people I know who work on toolchains.