A glass or two of wine is good. It seems to be partly due to "hormesis" - the substances in the wine are like a mild challenge to the body that raises its defences and thereby encourages health.
Ferris's diet is about weight loss pure and simple. The once a week re-feed days where you eat large amounts of any crap you want are a good sign long term health is not a big concern of his. Legumes aren't as bad as grains in their insidious effects but they do contain lectins and phytates, both fundamental concerns on a paleo diet (though somewhat reduced by soaking for long periods and thorough cooking). Also if you are going for more carbohydrate to support exercise, could I humbly recommend fruit or starchy vegetables instead? If you're not exercising (very) large amounts, there's just no need for the amount of carbohydrate you get in beans, and the repeated insulin response to them compared to other paleo foods is not your friend if you are aiming for a long healthy life. For long term health, having a very low fasting insulin level is ideal (and a good predictor of other health measures like hsCRP, lipid profile, blood pressure). It also makes you feel mentally clear all day. Ferris is a "biohacker", fun but fundamentally in it for the short term.
I would suggest trying a month adhering to all the little exclusions on a paleo diet, however odd they seem, and then seeing how you feel. You may find you feel amazing, and if not, you haven't lost much in the experiment.