Update:
Ended up keeping the booking made through nationalcar.com.mx, as the ~$200 savings over 5 days were worth the risk. The reservation never appeared in my Emerald Club account, nor was a phone agent able to locate it.
My Emerald Club number (entered in the online field) was listed on the contract at pickup (PVR), and while the rental never showed up in the app, both the rental credit and 1-2-F points (800 of them!) posted within 48 hours.
