How do I include a non-technical critique or line of thought in a technical doctoral thesis without being off topic?
An excellent doctoral thesis in software engineering must have passages of non-technical thought, the more the better. Such passages make the work accessible. Of course, technical aspects must appear to. The non-technical passages complement the technical aspects, the former provides the story of how the latter came to be.

To explicitly answer your question: Non-technical parts aren't off-topic, include them wherever necessary, just like technical parts, I don't see a need to explicitly distinguish between the two, the author will know.