I have been told the same thing about "Full Fare" Pax getting priority over discount fares on the upgrade list.
What happened to you is why a lot of agents don't want to tell a passenger where they sit in the upgrade pecking order. Most of the time I ask, I am told "It looks good" or "It doesn't look good". I usually have to press them to find out where I stand exactly.
As far as the elite guide goes, It doesn't mention a waitlist order at all. I would bet that this omission was well thought out.
I think that the Y class issue comes up infrequently due to the immediate upgrade that you can get upon ticketing. Unless the flight is sold out in A at time of ticketing, a Platinum member purchasing a Y ticket will get the F/C seat right away.
I have one rule, if I can't upgrade in advance, I will get to the airport as early as possible. That way I get a good spot in the upgrade waitlist.
BTW,
BF is everything they say it is, isn't it!