They will be better than what you buy in the store, because you raised them! I really can't say that the flavor is a whole lot different, but we let ours get bigger than store bought, and so there is more meat on those bones. We have never raised chickens in tractors, only inside, but we have eaten some raised in tractors and really wasn't all that impressed. They tasted a bit gamey and were tough. Ours are nice and tender. I know there are a lot of folks suspicious of commercial feeds, but we have no problem with the feed we are buying, our concern is the way the commercial chickens are processed, and the fact they are not big enough. When we do the processing, we know how healthy the chicken is, how they were killed, how quickly they chilled down, and what the water looks like that they are soaking in.
To reduce the ammonia smell just add more bedding, it will help capture that nitrogen for use in your garden later. They do create quite a bit of waste, if you carry 50 lb of feed and water in, you are going to carry most of it back out in one form or another.