As it currently appears in the game manual:
"Tokens
Some keywords have a side-effect, that requires a token counter. Player can choose up to three token counters for each deck in the deck section. It is possible to assign the token counters automatically by selecting the "Auto" button. Playing a card with keyword, which is associated with the token counter, will raise the value of the token counter. When a token counter reaches 100 a side-effect will happen and the token counter will be reseted to 0. This side-effect takes place directly after the card effect of the played card.
Let's take the Alliance keyword for example. First you need to set one token counter to Alliance keyword (in the deck section). Then you normally start a game with this deck. When you play a card that has Alliance keyword, it will raise the Alliance token counter. When the counter reaches 100, it will add a Production X2 to the effect of the played card and will be reseted to 0. By paying close attention to the token counters, you will be able to make good combos of card effects and keyword side-effects. For example Soldier and Ceremonial guard or Alliance and Stilshrine of Miriam can make good stock boosting combos."
Nowhere in the entire Tokens section is it mentioned that the rate of accrual is based on the number left over in-hand. On the contrary, it claims that simply playing a card with a keyword is enough to increment the associated value as long as it was selected. According to the text above, playing an Alliance card will always add Alliance tokens. This is misleading and, in the event that the played Alliance card is the only one on hand, false.