I'm thinking of recipes like chili, which have a "brothy" component to the finished recipe. One would hope that adding dry beans to an appropriate amount of liquid, loaded with aromatics and spices, would add flavor directly to the beans as they cook. I can imagine the counterpoint being the differing amounts of liquid that dry beans might absorb, according to variety and age, but it doesn't seem as though that would be hard to compensate throughout the cooking process.
Because the amount of liquid, time, and environment needed to cook dried beans will affect the finished result.
Beans absorb and require a very high proportion of water. A lot of people either presoak dried beans overnight to help shorten the cooking time. For your hypothetical chili, you are adding on hours of cooking that cook turn the rest of your ingredients into mush.
Another factor is that acidic ingredients increase the cooking time for beans. Cooking dried beans in your chili would increase cooking time because of the tomatoes.
You have to soak beans for at least a day before you cook them. I usually do two days. There are in these two days also several changes of water as the bad solids have to be removed. There may also be some time spent trying to remove any stones that may be present in your beans. Depending on how your dry beans are sorted by the manufacturer this may be a concern.
Some people use Bicarb in the soaking also, if you do then there are several rinsing involved in removing the bicarb before you cook the beans. Then you have to cook it for two to three hours after the 1 - 2 days of soaking, then you have to cook it in the sauce for 30 - 60 minutes so that the generally flavorless beans can take the flavor you want to impart on it.
It is quite the process to cook beans and it is not something you can just do. It takes a certain amount of effort and meal prep to make. This is why the recipe calls for beans that have already been cooked.