It appears BoP is adding potion/effects 32 & 33:
32,potion.paralysis,biomesoplenty.potions.PotionParalysis
33,potion.possession,biomesoplenty.potions.PotionPossession

I can't find a configuration file for those while thay overlap with ArsMagica2 potion/effects:
32,Water Breathing,am2.buffs.ArsMagicaPotion
33,Flight,am2.buffs.ArsMagicaPotion
...

My problem is the ID changes when adding ArsMagica2, I would prefer to have both in fixed positions instead of jumping around.

I'm using:
Forge Mod Loader version 6.4.49.965 for Minecraft 1.6.4
BiomesOPlenty-universal-1.6.4-1.2.1.416.jar
AM2_1.1.1c.zip

It's not missing. We create our part of the potion array and stick to it. There is no need for it to be configurable.

In addition, we add to the end of whatever is already in the potion array. If Ars Magica did the same then there would be no problems here.

It might be added at the end but it still change position so whenever we add a mod that change the potion array, BoP effects are changing position. The latest creates world corruption, notably of players/entities.
Also, keep in mind that BoP & ArsMagica aren't the only mods extending the potion array size, see for example DragonAPI from RotaryCraft.