We understand quite a lot. When the universe is 100 seconds old the only paired production are electrons, neutrinos, and other light particles. Within the first few minutes of creation protons and neutrons fuse into nuclei. By the time the universe is about 15 minutes old, much of the hydrogen and helium had been formed.
Quarks are transitory. Creation of protons and neutrons continued for about 10-4 seconds.
The radiation era lasted for 50,000 years. Which is why in the link you are basing your hypothesis upon they said the different decay rates could not have been responsible for a universe being filled with matter instead of radiation.
So if the matter and anti-matter were annihilating each other for 50,000 years and quarks only lasted for 10-4 seconds, then the different decay rates that led to a universe being filled with matter instead of radiation would have had to have occurred with protons and neutrons.