I recently missed a flight because it was cancelled due to inclement weather. I was rebooked on the next flight but Economy was the only class available. Economy SCs were added to my QFF account but I sent in the original boarding pass (booked in First) and because that was the class I was 'booked' in the SCs for First were added to my account. The operative word in the T&Cs is that 'status credits are earned for the class booked'. not necessarily flown.
Dede - i think you were lucky to get the extra credits.
When an instant upgrade (YUP or KUP) cannot be confirmed because of a change in flights (say because of bad weather) you can accept the offered alternative if this is in economy, OR, you can wait until the next flight when First is available.
The class you are booked in will be the class you fly. When you have an irregular flight you are then reBOOKED in economy, and that is the SCs you should receive.
The Ts and Cs you quote really refer to the situation of upgrades, where you have a base economy fare but have used points, or are otherwise upgraded to a higher cabin. Those Ts and Cs make it clear you only earn for the original cabin booked, not whatever you happen to have been upgraded to.
For the AA instant upgrade fare you have booked economy but the 'eligible booking class' (for SC earning) is A or P. BUT if A or P is not available (only happens in irregular operations, or a one class jet), then the eligible booking class becomes Y (or L sometimes for a one class jet). In that case, you have paid Y, and are seated in Y, and SCs should earn accordingly.
This is always the danger of doing a status credit run on YUPs. If you have to change a flight you could end up in economy and lose your SCs.