No, I don't think Burdick is referring to the T206 Wagner when he says "Pontifical Standard" here. At first glance, the wording of that sentence does seem to suggest that the "Pontifical Standard" is included in the "wants in the #521 set", but it could also be referring to two separate elements of the four cards that Wagner had sent to Burdick -- one or more cards from #521 (T206), and also a Pontifical Standard card from another set.
That interpretation is made more likely by the fact that "Pontifical Standard" had a specific meaning -- in the late 1800s, it referred to the flag of the Pontifical States, or what we today know as the Vatican. There were numerous tobacco card sets of national flags in the 1880s, several of which included the Pontifical States flag, and I assume that Burdick is referring to one of these. I haven't been able to find one that's explicitly labeled "Pontifical Standard", but the N195 Kimball National Flags set includes a card labeled "Pontifical States" -- #9 at the following link:
http://www1.coe.neu.edu/~dan/N195/go.html
That flag also appeared on a card (which I have) in N126 Duke Rulers, Flags, Arms of All Nations set, though there it's labeled "Flag of Papal States" (#35 at this link
http://www1.coe.neu.edu/~dan/N126/go.html
It wouldn't make sense for Burdick to refer to the T206 Wagner as the "Pontifical Standard", even if the card was as well-known in 1939 as it later became. "Pontifical" means "having to do with the Pope".
Also, as I pointed out in a post last week, Burdick thanked John D. Wagner in the October 1, 1948 for donating a T206 Wagner to the collection that Burdick was giving to the Metropolitan Museum of Art:
http://net54baseball.com/showthread.php?t=240887
If that 1939 letter referred to the T206 Wagner, it would imply that Burdick had a Wagner but then traded or sold it before 1948. But I don't see any evidence of that in Burdick's voluminous writings from that period, though there are some mentions of how rare the Wagner was, including in the October 1, 1948 article linked to above.