Those holes should be filled with at least with masonry cement. You can get it at the big box stores, it is sold in 60lb bags for a few bucks. It does not matter whether it is fast set, type S, it just needs to be masonry cement. No need to mix the whole bag. A 5 gal bucket to mix it in and a Tupperware(r) container or large coffee can will hold about what you need. Get a margin trowel, also at the same store you get the cement. Mix it to a peanut butter consistency and carefully place it around the edge of holes. With a little coaxing it should go in.
DO PROTECT the roof, it will stain it, or keep a garden hose on the roof with you. You will need something to keep the roof clean from the chimney crown material.
Do not let the material you use to protect the roof be the same material that throws you off the roof. Stepping on a loose tarp will do it fast. Plywood acts like a skateboard. Be careful!
The way the chimney crown material works, you may only need it to get hard overnight before you apply the chimney crown material