Bomb tokens are placed on the map faceup. The number revealed indicates how many full game turns elapse before the bomb explodes. At the beginning of each turn, replace the token with the next token. For example, a bomb token with the number “2” on it would be replaced with a bomb token with the number “1” on it. If the number “1” is on the board, it would explode at the beginning of the turn, rather than being replaced.

And then later:

A bomb that is disarmed is turned facedown and remains in place on the map , but will not explode. A bomb that is rearmed is turned faceup and begins its countdown again from where it left off.

And again:

When a bomb explodes, discard the bomb token from play ...

A "1" token is supposed to mean 1 full game turn. If it explodes at the beginning of the following turn, then it is not 1 full turn.

A "2" token is supposed to mean 2 full game turns. How do I do what the scenario says if the "1" token was either disarmed or removed from play?

It does not work at all as it worked in V1. In V1 it was "really" full game turns and you did not replace tokens with other tokens.

The Matriarchy player wins by detonating three bombs. The other player wins if there are ever two disarmed bombs on the map simultaneously.

What about killing everybody? Killing the Matriarchy army was a victory condition in V1...