Part of the confusion might be from the game using confusing terms for everything. If you've ever shredded cards for trading, flairs, etc those will all count as collected but won't show up in the card count when you search through the Dex.
I made an exhaustive list of all my cards from the extensions in a spreadsheet, the total count is consistent with 2617 cards, which is the reason I was trying to understand the mismatch in the first place.
Sorry I'm not of more help. From within the game my numbers all seem to add up if I filter by the same criteria you're using. Either you have a card I don't have or you have some kind of glitch going on lol.
Edit: Actually there is a one card discrepancy, interesting.
Another count the trew me off was that the sum of the card count of the two first extensions (counted separately) was not equal to the number of cards when filtering the two extensions together.
I figured out it was because "old amber" is present in both and was counted only once in the combined filter and once in each of the individual filters which amounted to counting it twice when summing.