Excellent that you are asking these questions!
Trying to grasp magnitudes and scales of "things" and how they relate to the mechanics of this reality (the rule-set) is not something that should be done lightly. You can't really just use your own "common sense" thinking of scale and magnitude and then apply to all of reality, and then expect things to work in a certain way.
The answer is that your sense of scale ("trace", "less abundant", "third decimal place") is simply wrong related to the exact mechanics and processes you are trying to understand. The photosynthesis process (and the Calvin cycle etc.) simply operates at a scale that is different than what your expectations and beliefs would suggest.
Just try to imagine that for the complex processes and interactions that eventually leads to the construction/accumulation of 'complex carbohydrates', a 0.04% may actually be huge
! Well what does huge even mean? It just means that unlikely to be a bottleneck in the process. I'm not saying that you have to think it's "huge", but you need to imagine that it might as well could be.
You need to apply the same kind of humility and openness towards how the "third decimal place" change in something can have a strong effect on something like climate..
It can very easily..
If you need to have some even more 'crazy' examples of scales and magnitudes, look up the matter-antimatter asymmetry problem
. Why didn't all matter and anti-matter annihilate each other a short time after the Big Bang? It would have been expected, as there should have been created equal amount of matter and anti-matter.. But we can calculate that about one particle per billion survived, and thus we are here.. if this tiny asymmetry didn't exist, the Universe would just have been ocean of photons, nothing else.
What about the fundamental physical constants, such as the Fine-structure constant
(characterizing the strength of the electromagnetic interaction between elementary charged particles)? A tiny change to this constant (or any of the others representing fundamental forces) would result in huge changes, from stellar fusion being impossible, to making it impossible for water to exist. This related to the Anthropic Principle
, which in part discusses whether this "fine-tuning" of the Universe is just a survivorship bias (that the Universe must be compatible with life, since we can observe it) or if it has greater implications on whether life or consciousness is some integral part of the Universe.. interestingly, the Universe being a virtual reality is one of the possible solutions to this philosophical problem.
There are countless examples of scale and magnitudes defying "everyday thinking".
To summarise: Much of physics (or biochemistry, or any other science) defies the "everyday thinking" that most people are very used to.. part of the training involved in becoming a (good) scientist, is to humble yourself and discard the sense of comfort through relating to the world with this "everyday thinking".. and discard one's easy reliance on assumptions and beliefs in how things work. It also helps to practise critical thinking.
The scientific literacy is unfortunately quite low in a lot of places in the world, including the U.S. An uneducated citizen is easier to manipulate than an educated one, and if you want your way as a politician in a democratic society, one solution is to sabotage the education system, allow anti-scientific teachings, and shape people as you want them as they grow up. Let us just say it's in no way conducive to growth towards a lower entropy society, nor individuals.
If you want to, the answer to your question could be a whole journey in itself. A journey (and effort!) of getting rid of beliefs, and getting a new and deeper understanding and appreciation of those who dedicate themselves to understand the questions you asked, and the whole personal process which YOU also can experience. This would benefit you much more than just a super technical answer to your question.