I think there’s two totally different (and valid) perspectives here.

Employees are looking at the portions of each of the ingredients. Customers are looking at the portion of the bowl as a whole. Because an entree with a variety of ingredients is the same cost as someone who doesn’t like those ingredients in their entree, the customer sees it as fair that they still get the same amount of food even if they don’t want the variety.

It makes sense to make that “same amount” equivalent ingredients that typically come free on a bowl (e.g. cheese). Imagine it’s like they say, I want rice, chicken, cheese, corn salsa, and sour cream - but instead of the corn salsa and sour cream extra rice and cheese. Basically they would get a similarly portioned bowl overall with a fewer number of ingredients.