The sense is in the marketing/selling. People are more likely to use 2 TB's than 2 Baffles, ergo you need 2 Mist Hunters if you dont want to wait for the Imp Vets. As for the tokens, I believe a lot of these are just space filler. I mean do you really need 3 50 numbers and 3 51 number tokens?It feels like a last minute change. There makes no sense on including two tokens and only one card, as you cannot place more than one token simultaneously with a single Tractor Beam cannon.
Actually you do need 3 of the number tokens, they are not just space fillers. Two go on the base both showing the same side outward and the third is placed on the corresponding pilot card showing the same side up. This is for differential purposes in case two people are using the same number tokens. You need two for the base because the tokens are double sided. When viewing a ship with only one token on the base, it could be accidentally be confused as your opponents ship at a glance if you see the opposite side showing.
Example: You use the dark side to indicate your TIE swarm and your opponent uses the light side to indicate their TIE swarm. With only one number tile, your shop could be mistaken for your opponent's during play as you will eventually see the 'back' side of the tile during manoeuvring.
