My guess is that the food is clouding the water by itself or the fish is producing more waste from over feeding. Ammonia build up can be a problem in any fish tank. You also may have a different mineral content in the water in your town. The conditioner you are adding may discolor it too, or react with the food.
Your pet store should provide free water testing if you have a question. Go with the experience of the people in the store (and I'd say to go to a small pet shop owned by real pet people instead of the mega-stores staffed with high school kids!) and don't follow what's on the directions of the product all the time. Kind of like shampoo instructions to "lather/rinse/repeat" or toothpaste ads showing a whole long stripe of toothpaste which are just designed to get you to use more product, the fish supplies can tell you to use too much. We found that with our fresh water tank for community fish - we used much more stuff in the beginning because it was a big seller for the store. Don't use Google. Use the people who want your repeat business.
The fish is going to eat whatever you put in there. In nature, it would be competing with other fish, but in your house he's the only one! They don't stop when they're "full" - they aren't that sophisticated or disciplined! They eat if it's there.
One other thing with betta fish is that they jump. Don't fill the container too high up unless it's covered. We found our fish dead on the carpet because no one told us this!
Remember that every time you remove the fish and push it in another container, you cause it to have stress. If you're putting him in one kind of water with a certain amount of conditioner (or none) and then putting him back in water with chemicals, you stress him out again. He's not going to live long if he's not stable.
I don't understand why the small tank has to sit all day for the water to reach the same temperature as the little container. Room temp is room temp. It doesn't take that long to equalize. If you aren't sure, use an aquarium thermometer. But while you're sitting there waiting all day, the fish is in a different container than what is supposed to be his habitat. His fish poop is contaminating that while you wait for water to come to room temp. I don't know any fish store that recommends that, so verify it with the place where you bought the fish or another place that you plan to use going forward.