Ammonia comes from decaying protein and urea. If you compost mostly brown stuff, for example autumn leaf litter and
wood chips, then there is not much protein or nitrogen to be converted to ammonia. The more green vegetation you have, the more protein there is and that can give off ammonia as it composts. When you add animal manure to the mix, you jump to a whole new level of nitrogen availability, because now in addition to undigested protein that may be present in the manure, you also have urea, each molecule of which can give rise to two molecules of ammonia.
The more nitrogen you have in your compost pile, the hotter it can get (more nutrients available for the bacteria to grow on), and the more ammonia that it can give off. As your link describes, sometimes you err on the side of too much ammonia and it kills the plants. There are too many variables here to give you a simple
answer; ambient temperature and air flow are two variables that you have under your control that you can use to manage your greenhouse. If it's too cool, you add more manure and the compost pile heats up. If it's getting too hot, you can increase the air flow during the day and maybe stop it at sundown to keep the heat in.
A simple temperature probe in the compost pile could help you arrive at a workable solution. You can get a cheapie indoor/outdoor digital thermometer and stick the outdoor probe in the middle of the compost pile and have the indoor read the ambient in the greenhouse. From those measurements, you can get an idea of how much heat (and indirectly how much ammonia) the compost pile is producing.