Ok, so, my DM and I have been looking over this, and reading the FAQ. We noticed that this question had been addressed in there, and the Sage had actually backed up his answer:
'If a character no longer meets the requirements for a prestige class, he or she loses the benefit of any class features or other special abilities granted by the class.' - Complete Warrior, 16.
Credit goes to the Sage for pointing us to this section.
From this, it's apparent that our Beholder Mage can't actually polymorph out of his form if he wants to stay a Beholder Mage.
Obviously, this places a limitation on a number of classes in game. Standard Shadowcraft Mages are now forbidden from Polymorphing if they want to keep using their abilities (including the spellcasting they gained). Similarly, Arcane Archers have to stay elves, and Chameleons have to stay human.
SorO_Lost, I personally view the Sage and CustServ as upper and low court judges, respectively. The D&D rules themselves are the first port of call, then the Sage's interpretation of the rules - assuming this interpretation is backed up by evidence. If the Sage's interpretation is not backed up by any evidence, then it can't be said to be a proper opinion. Similarly, if in the course of answering one question, the Sage makes an offhand comment on another area of the rules, the same weight shouldn't be given to the offhand comment as to the primary answer to the question. CustServ decisions, similarly, are also persuasive, though not nearly to the same extent as the Sage. Additionally, they can be overturned by the Sage, and both CustServ and the Sage can be overturned if they get the rules blatantly wrong. That is to say, they can advice on 'grey areas', but can't blatantly contradict the text of the books.
Hope that helps!