How does the randomizer work for insurgence? Is it a random encounter for every encounter or is every pokemon randomized where one pokemon would appear instead of another one for every encounter where the original pokemon would appear ( For example, where a weedle would be encountered a butterfree would be encounter instead for everytime a weedle would normally be encountered?

Random encounter for every poke, items are randomized, and necessary items for the game aren’t. So, in theory, you can get a Giratina in the beginning of the game.

They are not area-based, it always cycles through every single one of the 921.