If the treatment is relatively mild, the dropouts are comparable between groups then I am not sure that per protocol will introduce much bias. What do you think? In that case it can be a decent tool for enhancing power, although the results will always be considered “post hoc” and “hypothesis-generating”.
From experience I would say that intention-to-treat analysis is the standard in large studies of drugs and supplements, while per protocol is often performed as a secondary analysis. Especially when ITT is marginal and you have to go fishing for some results to report and to justify follow-up research.
While I agree with the logic of avoiding subjecting highly unsaturated oils to heat we do have to be cautious here with speculation.
When you say things like that: “Nonetheless, if these things are poisonous at high concentrations, they’re probably not great at low concentrations.”
It does not clearly follow that such a dose-response exists. The word “hormesis” gets thrown around a lot in the lay press, and there is actually some truth there. Plenty of moderate (even genotoxic) stressors have health benefits at lower doses. Of course, I would not gorge on lipid hydroperoxide based on this, because we have better evidence-based “hormetic” stressors, but it also does not follow that lipid oxidation products at low doses are harmful.