I understand what you mean. I try to minimize the time out of water by using a second container without holes that the first will slip into. This way they can be in water right up until I am ready to place in second tank then just lift the container with drain holes out of the other to drain the water out. Into the tank they go. You can't use the bag method with TT since you don't really want to transfer the water.
As far as ammonia goes, it usually isn't an issue in those 3 days but I do dose Amquel or Prime if I have more than a couple of small fish just to be safe.
By the way, not trying to convince you to use it, just sharing that it is a safe and effective method of getting rid if ich. How you feel about TT is how I feel about copper. I don't like copper since it is basically a poison. But I will use if I need to.
Sorry to the OP that I have taken your thread off topic somewhat. There are different ways to skin the proverbial cat, research and pick what works best for you and stick with it. So much easier to take care of diseases before they end up in the display tank.