People buy Y fares for various reasons.
For those who are already elite, the confirmed upgrade at time of purchase is an obvious motivating factor.
Others, including many of the elites who may be buying these fares, value flexibility. A few $100 change fees can eat up the difference between a lower fare and full Y. And, of course, a full Y can be refunded if you decide not to take the trip or change your plans in the middle of your trip.
Finally, don't forget that many firms collect an administration fee on reimbursable expenses not included in an expense schedule. 10% of a Y or D fare is much more than 10% of an S fare.
I need flexibility and I want FC. I am constantly changing and missing flights. That means that I buy the flexible D fare, unless Y is cheaper. In two rare instances during the last year, I have bought full A. In any case, I can not recall the last time that I actually flew on my originally ticketed flight.
jh