So, let's continue with your example of a drug being given to the rodents. Now, you want to control diet -- you don't want your control group eating differently than your treatment group. This ends up being relatively easy to do with laboratory rodents, they aren't popping down to McDonalds for lunch or lying in their food diaries, like human subjects might. You buy your rodent food from one rodent pellet supplier, and you don't change brands or SKU during the experiment, and voila, control.

And this works fine if the drug you're studying works identically given all rodent diets. But you don't know that it does! You're not controlling for the variable of diet in the sense that you know the effect of the variable of interest across all possible diets. You know how the drug works conditional on one specific rodent diet. And if you're not putting what brand of rodent food you use, and that causes replication failures, that suggests that you don't understand the effect of the drug as well as you thought you did. And if you have an entire field of research that undergoes such replication failures often, it's fair to start wondering how much of what gets called "science" isn't the study of the natural world but the study of the very specific sets of conditions that happen in labs in American and European universities.

Yes but the things they mentioned would be bizarre to control for the other way.

Would you expect the tests to be done, then again but with both rats hearing the person upstairs installing a new microscope, then with a regular fire alarm, etc?

Describing the food given is quite a step away from describing how frequently the fire alarm goes off.