They’re in place because of past abuse when there’s no cooldown.
There are two types of cooldowns you see:
1. The 24hr cooldown that is applied after participating in an Alliance Challenge.
2. The AvA cooldown, which now prevents you from participating in AvA for a different Alliance than the one you first started with.
The first one is to prevent abuse of Alliance Challenges.
In the past, we had players join Alliances in rapid succession, joining ten, twenty, or more Alliance challenges in the space of a few hours.
They’d take #1 spots away from regular Alliance members, and farm challenges that way.
We chose to introduce the 24hr cooldown after participating in a challenge to curb that.
The second one is to encourage players to commit to a specific Alliance during an AvA phase.