I agree that there is a lot of randomness in regards to quality, but it is not strictly random. Having the "Green Thumb" weights the "range of randomness" to a slightly higher range. It's not very much and you really have to garden a lot to even notice at all. Simmers who only garden casually would likely never even notice the difference, and for them these would likely be two trait slots that would be better used for something else. And once you've got planting materials that are Perfect, there's not much point in having these traits at all.
The LTR "Super Green Thumb" helps a little bit more, however. You'll end up with perfect plants, which will produce perfect produce, a good deal sooner than you will without it. Especially with the more stubborn plants like Life Fruit.
It's worth noting that everything I've discussed in this thread doesn't include talking to the plants to increase their quality. This is something that I don't often do, since my gardener sims tend to have jobs or are in school, and sometimes have children. It's not uncommon for them to be the household cooks, as well. Thus, they normally have other responsibilities that they need to attend to, and just don't have the time to do this. Also, my gardens tend to be somewhat large, so talking to each and every plant to raise it's quality just isn't practical for them. But during the rare moments when they have nothing to do, I do send them to talk to the plants that take longer to grow since it takes a lot longer for these plants to reach perfect quality.
I've also seen no direct affect from traits on the quality of money trees.