I use AlphaLoot for 2x loot.  Would this plugin work with AlphaLoot or does it need to be vanilla loot tables?

Timed Progression should work fine with any loot table modifications because it does not consider or change what is in any given container until it is looted. Once a player loots a container, it checks each item to make sure it is not locked and replaces any locked items with items from the previous phase of the same category. It preserves the stack size when replacing locked items that are in stacks.