Pretty much any product that is safe for leather will work just as well on the vinyl portions. After all, most leather in mainstream cars these days is PVC-coated anyway. Really anything safe for vinyl would technically also work, but may leave the surface slick and greasy to the touch. Something like 303 would theoretically protect the surface. Using whatever leather or vinyl safe product you choose should cause no harm.
On a couple of previous vehicles when I noticed something stuck in one of the "holes", I gently used a pin to clear it. Haven't yet had to try it on the Passport. Proceed with caution if you do this.
I'm not sure how Honda describes the leather seats, but some manufacturers use the term "leather seating surfaces" to designate that not all the seat is leather, only the part you sit on. I read recently someone sued Mercedes because their terminology implied the entire seat was leather. They won the lawsuit and the manufacturer had to recover the entire seats in leather.