I've run a campaign with a Magus in it, but I disallow my players to make gold selling items. Ok, I don't exactly say they can't go and sell items, but if they make noises in that direction I point out the many evil dwellers who would like to enslave gifted crafters. It usually does the job.
As for pricing, it is true that it seems like Magus and Alchemist items differ in terms of creation costs, just in man days a Magus takes just about twice the time if memory serves right. There's some information on Castle and Ruins regarding how much a court mage costs per month, you could just add that monthly figure to the Alchemist cost of an item I guess.