Niacin therapy is effective at reduce heart disease risk due to lowering LDL particle numbers and triglyceride levels, not due to increasing HDL. The risk of diabetes can be minimized by eating within 2 hours of taking niacin and avoiding digestible carbohydrates 3–6 hours after, unless another dose of niacin is taken. Liver toxicity can be minimized by eating a diet rich in methyl donors like folate, vitamin B12, methionine, betaine (trimethylglycine), and choline.
Improving riboflavin status (via supplementation) may make MTHFR work like it should, since the 677C→T mutation simply reduces its ability to bind with its riboflavin-dependent cofactor (FAD).
It’s literally addressing the cause (making MTHFR work like normal) rather than the symptom (supplementing with 5-methyl THF because you make less of it).