Good thoughts everyone, this is certainly a tricky situation. What's even more tricky is that in the 40-card set, each team is given 10 cards and each "team set" has it's own numbers 1-10. It's not a 40 numbered set. You can see an example here: https://blog.paniniamerica.net/2014/01/21/hot-off-the-presses-panini-america-readies-commemorative-super-bowl-xlviii-sets/
It seems that the 40 card and 20 card sets feature the same cards for the Broncos/Seahawks but just one set includes the NY/NJ teams and the other doesnt.
I think the 40 card set would be a base and the 20 card set would also be base. It wouldn't seem to make sense to have the 20 card set be a base since it is the exact same cards. But at the same time I can see people wanting to collect only their teams and given the overlapping numbering, Panini is almost treating each team's cards as it's invidual set.
In 2015, Panini released Super Bowl XLIX cards and treated each team as separate sets: https://blog.paniniamerica.net/2015/01/19/panini-america-ready-to-celebrate-patriots-seahawks-with-super-bowl-xlix-card-set/