It's really difficult to know what you are talking about. Half your story sounds as though she was getting your wish list/putting you on a waitlist and the other half sounds like a special order. However, special orders are generally only offered to the best standing clients so it would be very rare for a walk in to be offered such. And you say blue Encre was a choice for you but blue Encre was not on the special order available color list this year so you were not being offered a special order. In my opinion, the SA was trying to get you to select a combination that she would then put your name on the wishlist for. This is not an actual order. Your name would be on the list and then when a bag of that spec eventually comes in, they would go down the list and look at the names signed up for that combo and then assess their profile to determine who to actually offer the bag to. To even further confuse the situation, both blues you refer to are current seasonal colors and are unlikely to still be in active production "2-3 years" from now.
I believe the SA was trying to get you interested in the brand and the beautiful leather types available and was genuinely trying to recruit you as a client but in doing so probably mislead you a bit as to how the obtaining a Birkin process goes. In their mind, 2-3 years from now you are either a well established client, "worthy" of a Birkin offer, or you've fallen off the face of the earth and have forgotten about your birkin "order". The "France doesn't make enough bags to supply our store" tactic is a common excuse for why walkins can't purchase a bag that day.