American's own site indicates that's not the case for 500 mile upgrades. Although if other Exp's are upgraded at T-100 and you buy a Y fare at T-<100 I'm pretty sure they won't claw the upgrade back from a cheaper fare Exp.
It's under step 2 in this link:
http://www.aa.com/i18n/AAdvantage/el...desContent.jsp
"If an upgrade is available, we'll confirm it before departure based on your elite status level and the order it was received
Fares booked in Y and B are confirmed within each status level first, followed by all other fares."