Not sure if you want an interpreation on the actual rules or just houserules.
I don't play any houserules but as convuluted as the Allies deck is getting, I am not sure any interpretation is 100% correct.
To build it: If you combine multiple expansions, shuffle all the Allies together. Randomly keep 11. You are allowed to look at who is kept. Reshuffle and form the deck. These are the only 11 playable this game.
If you have an Investigator that calls for a specific Ally, such as Ashcan and Duke, then Duke is part of this 11 card deck. Or to put it more clearly, take Duke, and randomly select 10 other Allies to form the starting deck. There will never be more than 11 Allies in the game. If someone draws a random Ally, like Leo Anderson, they randomly draw from this deck of 11.
Encounters: Since you are allowed to see who is in the game at the beginning of the game, we allow you to look through the Ally deck when you run across one in an encounter. (This may be the first instance of us starting to houserule - but we just don't think we should be that restrictive when we can just as easily write down the contents of the Ally deck). If we don't have access to the Ally, then we decide at the moment if we want to take the "Plan B" reward from the encounter.
Charlie Kane disrupts everything. We have never gotten an official answer on this one. My opinion is that he starts the game with a random ally from the deck of 11 available just like Leo. Second interpretation is he can randomly take from all 34 Allies. I do not believe the interpretation he can take whoever he wants is correct. It is, afterall, a random Ally and if he could select one, he would probably always select the same one (Professor Rice).
As far as him gaining Allies, I think he can grab anyone that comes up in an encounter. That seems to be the rule he is breaking with his ability. Second interpretation is that he can only grab one of the 11 from that game that has gone back to the box. That seems viable and is inline with my setup interpretation. But it makes him considerably weaker. With the way we keep the Terror Track from moving, we rarely have any Allies get returned to the box. So we would never use his special ability. I do not think the interpretation that he "intercepts" any and all discarded Allies is correct.. His ability isn't worded in that way at all and would make him too powerful.
The only thing that is a question mark to me is Charlie and Ma's Boarding House. Since he gets to select his Ally, I would limit him to the 11 that are in the game. It doesn't sit well with me that he can choose anyone, even if they weren't boarding. I guess this remains in line with my setup interpretation.