I would go with a curb mounted skylight for a metal roof. I see far too many remodels where the GC and customer order deck mounts or self flashing types. They are doable but, the curb mounts are the way to go because your bending your roofing up to a wood curb with no flashing kit to get in your way.
What type of roof do you have ?
For example, the velux flashing kits do not work well with stone coated metal roofs, we usually fabricate out own from metal. The alum type velux kits are of a fixed size. We prefer to send sheet stock to the job and break it to the size needed.