Since when did any of the machines in the original trilogy display or align themselves with any one type of human behaviour?
Smith, Oracle, Merovingian, Persephone, Trainman, Sati, Rama-Kandra, Kamala, and the Deux Ex Machina itself. Basically every machine or program that mattered to the plot, aside from the normal agents, Seraph, and the Architect. All of them showed strong human traits even from the first movie. The machine AI evolved to reflect its creators, the human race. Programs are able to exist within any shell, be it a digital Matrix one or a real world machine. It makes sense why the Analyst is a jerkbot in Resurrections - we know the machines can have personalities and turn out to be petty assholes just like humans, which is why the whole situation in this movie came about, and it gives us a main bad guy that is relevant to why there's even a sequel in the first place.
I think the "binary" stuff is more referring to the fact that both Neo and Trinity must be caged in this new Matrix for it to work. You can't have the 1 without the 0, and vice versa - they both lose their meaning without the other, just like the system can't continue to function for long if one (or both) of them escapes. Same with light and dark, good and evil, yin and yang etc. - the whole franchise has been drawing parallels about polar opposites since the start, especially with Smith and Neo.
There are definitely some subtle nods to non-binary ways of thinking peppered throughout the script, most likely referring to gender identity, but I took that as more of a wink wink, "I'm trans and people should be okay with that" from Lana than a total agenda club... and I hate pop culture agenda clubs big time, trust me. There are enough anti-woke, anti-agenda messages in this movie that lead me to trust it. For instance, focus-tested, hipster marketing driven sequels and reboots are cringe trash, don't get brainwashed by social media, brainwashing is all around you, etc. etc.