The main thing to keep in mind is that you did not buy a ticket X-Y-Z. You bought a ticket X-Z with routing rules that allow you to route through Y on your way from X to Z.

The key is that AA is obligated to transport you from X-Z (not necessarily Y-Z) so that's why you can't just show up at Y and take the 2nd leg.

If you follow the advice to upfare you would be giving up the upgrade you already have and and paying the difference between first and coach on the whole trip (X-Z).