The conditions of carriage state:
Also, you may have to pay bag fees again if:
You are connecting on another airline
Your connection on American is more than 12 hours later
would that apply if I book it as a one ticket 16 hour stopover?
There is a stopover ticket that can work but much more expensive than a 2 ticket multi city....
From how they word the terms, yes, it would apply even on a single ticket stopover over 12 hours.
Especially if there are shorter connections available (if nothing shorter available, you have valid argument to not be charged twice).
Although if open to booking as a single ticket, I’d do that, then call / tweet and ask about the luggage, and if they say you’ll have to pay twice anyways, just void the ticket right away and start over.