When we booked an intra-Peru award ticket on LAN (with AA miles) last year, the total taxes were exactly zero. Nothing. Just the miles. So, unless things have changed, the domestic flight taxes are not paid. Our departure on AA back to the states was paid, and we got the sticker at check-in. Not sure what's up with that for malcolmkettering. I'd keep receipts and take it up with AA upon return. No use in stressing about it now- enjoy the trip.
Cheers.
Same experience on LAN. You pay it right after leaving the exit customs officer.