I'm actually taking it one step further. Assuming God and assuming the creation event was that of the atom (seems obvious, assuming God even in a YEC scenario), it's plausible that the system of everything is very good. It's plausible that the system cannot be improved upon, especially if the designer has a specific goal. It's plausible that they way things are are exactly as intended when atomic creation took place.
In other words, a designer of a shopping cart could finish up and see that it is exactly as intended while an onlooker could identify several design choices that are flawed by the onlooker's standard, especially if the designer's parameters are unknown to or ignored by the onlooker.
Where LM and I got bogged down was LM's implied and my explicit admission that we have no idea how to have done the atom better (assuming it was designed), especially since we don't know the full scope of the creator's desired outcome.