Hello, thank you for the well thought out ask! :D
While I understand where you’re coming from with your point, I do disagree. The order residing in the things mentioned - genomes, planetary orbits, etc. - is indeed present and is a local decrease in chaos, it isn’t an overall decrease in chaos.
To work with the example of planetary orbits and geological stratification (as those are the ones I’m most familiar with, haha), both can be shown to be local decreases in entropy caused by larger, overall increases. Stellar systems are able to form and settle into orbits as an aftereffect of gas clouds collapsing. The energy dispersal created in such a collapse is orders of magnitude larger than the energy organized in a planetary system.
The case is similar in geological stratification - the order arises as a result of millions of years of HUGE energy-dispersing activity. Volcanic eruptions, flooding, etc. Each of these things expends a great deal more energy than it ultimately organizes.
So perhaps the original statement was flawed. Negentropy can indeed exist at local levels, but only at the cost of an overall increase of the entropy of the system.