Well, technically not because otherwise, "oni" would be accusative and be "je" instead.
Now these machines are producing themselves
Not correct? Like in the matrix
No, that is not correct. That would be "Teď se ty stroje vyrábějí samy." or "Teď ty stroje vyrábějí samy sebe."
how would you say They make machines now? because that sentence is more likely to be used. rather than the machines.
In Czech that has the same translation as "They make machines now." In Czech we have the context to tell if now is really just now or it is regular since the last change a few years ago.