It's an interesting metric, you are mis understanding it.
As used it is an indicator of physical health,
but we both agree it is not useful in this case as western atheists generally choose their own fertility rate rather than let nature take its course.
A neutral 3rd party observer might have difficulty distinguishing between the voluntary adoption of an 'intellectual structure' whose adoption drove total fertility to zero and a spreadable physical ailment that did the same.
Voluntarily choosing sub-replacement fertility is a rational choice when resources are insufficient to properly raise a additional child. It is also a rational choice if one foresees such a shortage in the future and acts preemptively with a discrete plan for ones descendants to return to at least replacement level fertility. Finally it is a rational choice perhaps a heroic one when an individual is a known carrier of severe genetic disease and chooses not to pass that to the next generation.
Absent these conditions voluntarily choosing sub-replacement fertility is not rational as it is not synonymous with sustained existence.