Seychelles customs should not take long if you are first in line. Make sure you have a print-out of your lodging accommodations for faster processing. Unfortunately, the drive from SEZ to Bel Ombre is a solid 30 minutes due to roads. I think you have a good shot of making it, but I would try to call / contact the Jetty as soon as you land. If you miss the ferry, you can leave your bags at the jetty and easily walk to Beau Vallon beach to kill time.
Good luck and enjoy Seychelles!