The Henry roof coating won't afford water sealing to any through holes in the roof . The product information states that it is resistant to pooled water. That is not the same.
For a skylight, I'd use an adhesive specified by the Mfg of the skylight, some screws and washers to retain it (allowing for thermal expansion/contraction) and then seal any through hole in the roof membrane with Eternabond tape. AFAIK, Eternabond tape is the only sealing material that has a long life. After everything is sealed correctly, you could then coat the entire roof with a top-coat paint. I wouldn't use a silicone based product. I used an elastomeric top-coat that has held up well.
