Basicaly the way I understand how it is now is that the various currencys are now more or less how weighless things like "pre war" currency penciles cigs and so on are handled by FO3. (bascialy I treated anything that was weightless and non consumable loot as money, simply because (A) it Was Weightless and (B) you could "sell" it for real money. (bascialy you could have made penciles, prewar money, thoes passcards, and even individual cigarets as money. the game just defaulted to useing "caps")
This time around they probably looked at it and decided to make the vendors "want" one type of "money" more than the others as a trade default.
ok to clarify
assume each unit of currency has a base value of 1
and lets assume for now that you have
CAP$ (shorhanded to C$)
NCR$ (N$)
CLC$ (L$)
(not counting other currency)
its posible that a given "Semi independant" vendor may have the following BASE modifiers to the currencys "Value"
C$ 110%
N$ 90%
L$ 70%
This can posibly be further modified by the players actions, for example if he decides to do nothing but quests that help the legion, you might find that the player has added a global penalty of 20% to N$ and bonus to L$