I found at least part of an answer. The scientific paper at
http://www.plosone.org/article/info%3Ad ... 86849-g004 says the blue is a structural color and it's related to testosterone. I don't know the mechanics of exactly how it works so I'm not sure why certain mutations like ino and recessive pied don't develop the standard blue color, but I would guess that melanin is involved somehow. These mutations remove or reduce melanin, and I had previously guessed that melanin might be involved in the brown cere color that hens have when they're in breeding condition. So it seems reasonable so far.
I saw numerous websites saying that male budgies with testicular cancer or certain other diseases could develop a brown cere like a hen because they stop producing testosterone. Hens often have a pale blue or white cere when they're not in breeding condition and develop the brown cere when they're ready to breed. So male and/or female sex hormones definitely play a part in cere color.
I've been thinking about joining Talk Budgies myself to learn more about the species. It's OK if they're not super friendly to tiel people, I'm tough enough to deal with it lol.