I recently took a trip from PDX-SFO-ORD, PDX-SFO was an AA codeshare on AS metal, I was able to get both of my boarding passes from the AS kiosk.
A few years ago Alaska couldn't do this (or so I was told at checkin), but the last few times I've gone AS-AA I haven't had any problems. I've never had any problems when starting off on AA metal and switching to AS.