The Hall of Fame does indeed lists players under their "primary" team. They will list a player under every team they played for, but they will bold the players name for their main team. Whenever they count the numbers of hall of famers for each team, they only count the players that are listed as a primary player and not all the other ones, they will list the Bears with the most players at 26, not the Bears with the most at 30.
For example just ask how many Hall of Famers do teams like the Ravens, Panthers, or Falcons have... and you'll get the answer "0", even though there are HOF players who have played for those teams. Or look at the Cardinals website.. you don't see a big news article about Emmitt Smith going into the hall... because he's not going in as a Cardinal, he's going in as a HOF Cowboy who happened to play for the Cardinals.
Deon will likely go in as a Falcon(their first ever HOFer) and a Cowboy, like Reggie White went in as an Eagle and Packer.