I did some further research on this question and what I found is that originally (more than 100 years ago), there were a lot of different types of "catsup", grape catsup, tomato catsup, mushroom catsup, cucumber catsup, etc. The two most common types were tomato and red pepper catsup, where tomato catsup was made with tomatoes and pepper catsup was made from bell peppers. Tomato catsup was normally a spicy catsup and bell pepper catsup was a "sweet pickle". So, for example, here are typical early recipes:
So, in the above recipe we can see it is designed to be strong with cayenne pepper, black pepper, mustard, onions etc. Now compare to the bell pepper catsup:
So, we can see the bell pepper catsup is designed to be mild. Naturally, the inevitable happened: somebody just conflated the two recipes, mixing ingredients from both. The first example of this I could find was by one "Mrs. Scattergood" in an 1897 ladies journal:
We can see this recipe has the same weird combination of a huge amount of tomatoes with 2 small red bell peppers found in the Joy of Cooking. This recipe seems to be the origin of what ended up in the Joy of Cooking.
So, ultimately there is no logic to it, it is just some random lady from Albany randomly combining what should be separate recipes.