Hmmm.. ok so:
1) Are you suggesting the MoM knew who every single Dandelion would be, and individually coded them into his program? How, when Ava was the one who picked them all (for a long time doing so in secret)? And that... Doesn't sound like a very reasonable or efficient way to go about things, does it? Why would he need to "program" them in such a way in the first place?
2) Just because Player chose not leave with the Dandelions, didn't make them unworthy or unable of becoming one. Even in the middle of the Keyblade War, Ava still tells the player to leave the battle with the Dandelions, so they had the freedom and the approval to go whenever they pleased (provided they didn't die, of course). Also, it was technically Skuld and Ephemer who went to retrieve [Player] from the Keyblade Graveyard, and the latter was the one who did all the talking (and the one who actually took Player's hand) from what I recall.