The perception of "spicy" is completely dependent on the person. And there is a "tolerance building" thing going on too: what is intolerably hot for somebody not accustomed to heat might not even register for somebody who eats hot frequently. As an anecdote, I had a friend who started eating hot. After a month, she started asking the cook to use pure tabasco instead of tomato sauce on the pizza. After another month, she complained that the pizza was made with tomato sauce and the poor cook had to let her taste her from the bottle to convince her that the pizza was indeed made with pure tabasco, it just didn't have the same "kick" for her after habituation.
From your description of your soup only feeling hot enough for you after adding six habaneros with the seeds, it seems that you have developed an extremely high heat tolerance. And this would be an explanation for what you observed.
Six habaneros will contain a certain amount X of capsaicin. When your soup is fresh, the pepper has enough capsaicin concentration that you notice it and enjoy it.
But when you leave it alone, the broth dissolves the capsaicine (unlike pure water, the fat and maybe also the solvents from the vinegar enable it to do so). So you end up with a kind of "capsaicine tea".
But remember that you have the same amount X of capsaicine, this time diluted in litres of soup, as opposed to sticking all in one bite of pepper. So, now that you bite on the pepper, you don't get the heat. But when drinking the broth, its concentration is so low that it does not register for somebody with a high heat tolerance. From your subjective point of view, the heat has "disappeared".
The original intention of the recipe author was certainly that the whole soup becomes somewhat hot. And for people with less heat tolerance, it will work well. They will be able to eat the broth and notice the heat, even with much lower quantities of hot pepper.
For you, it seems that you still haven't reached the dose which will work for you in a soup. So you can add more capsaicin - either use more peppers, or find a source for hotter ones. If the logistics are a problem, buy them dried. But note that at no point will the whole soup taste as hot as the single fresh pepper (due to the dilution), and also that you will become habituated with time, just like my friend with the tabasco pizza.
Your photos each look like decent early attempts at bread making. I would encourage you to keep at it. While I think your process will improve (for example, you probably want to improve gluten development with further kneading or stretch and folds), nothing about your process would impact the flavor to the point of making it "unusual."
I would make two observations. First, you might want to take the temperature of your bread, at the center, near the end of the bake time. Just to make sure you are cooking it completely. It should be 190 - 200 F (88 - 93C). I usually bake darker. If I am using a dutch oven, I will remove the top at about the halfway point, leaving the pan and bread in the oven. I just like the flavor of a darker crust.
Second, the breads that you mention in your comment are typically made with a starter, or are enriched breads. These breads will have a different (and perhaps more enjoyable to you) flavor profile. You appear to have some of the basic technique down, maybe you want to experiment with a sourdough starter and a formula that uses a combination of flours, and allows for more flavor development. It will take more time, but the flavor will be noticeably different.
By the way, you can always make croutons or breadcrumbs with the loaves you don't enjoy.
Best Answer
"Capsaicin is soluble in alcohol, but very little in water. Because of the burning sensation caused by capsaicin when it comes in contact with mucous membranes, it is commonly used in food products to give them added spice or "heat" (piquancy)."
Time was your magic ingredient. More capsaicin became soluble. I find rich dishes have no surprise punch reheated:
"Food that's high in oil or fat dissolves the capsaicin, so it can't continue to bind heat receptors. ... Full fat sour cream or ice cream."