Edit 4: Ok! So I've discovered some things. There's something wrong with the Item Rarity Excluder specifically. Ellix's calculation worked for every one of my tests except the Item Rarity Excluder. So I'm currently making more Item Rarity Excluders to check this out.

Edit 3: Jelly just brought to my attention the fact that basic ingredients add 100 to the calculation. I'll be revising all of my calculations shortly. ;v;

Edit 2: Actually, Ellix's theory doesn't explain some of the scenarios I came across. Potions like the Wealth Potion, Mass Range Extender, and Potion of Evolution all took into account the quantities of ingredients when the game calculated the final grade. It also doesn't explain why in some of my experiments, the game rounds down when it should've rounded up.

Edit 1: Ninja'd by Ellix xD

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So, I just want to start by saying that my assumption of the way the game calculates averages is the same as Chris'. I assume that the game adds up the grades of all ingredients used, and then divides that by the number of ingredients used (and ignores non-grade items, such as the Starch Cube and so on).

Based on that assumption, I tested every potion with varying grades of ingredients, starting with the Item Rarity Excluder. So if the game is supposed to calculate averages the way that we believe it is, then I can confirm that there's something wrong with the calculations for certain potions. Below are my results for every potion.

(Don't read this, it's wrong lmao)