Not all cells will perform the same sequence of transcriptional changes. The paragraph you quote simply states that differentiation isn't a step change with all cells differentiating at the exact same moment. Rather, it's a more gradual change with cells each working on their own time scale.
Based on back and forth in the comments, I think that you might be interested in a deep mutational scanning workflow, for example dms_tools2 or enrich2.
These are built specifically for the kind of experiment that you are interested in, if I understand correctly. See attached figure from dms_tools2: