The thesis wants three institutionally differentiated layers. Section II says layers are jobs in a control transaction, not organs and not institutions. The brain is allowed to run all three through overlapping circuits.
Those counts fight. If the brain counts, "institutionally differentiated" is not required. If separate institutions are required, the brain example is one organ with three labels. You cannot use both to show that complex systems converge on three.
The count is the jobs. Westminster has many branches because the three jobs are implemented through specialized offices, not because there are more than three layers. The brain is the same point: one tissue, three jobs, as long as you can name the transaction.
"Institutionally" is just how polities happen to implement the split. The architecture is the jobs.
Then the thesis word is doing work it should drop.
The governance section maps family, courts, and the executive as the three layers — those are institutions. The brain paragraph says they do not have to be. If the load-bearing claim is jobs, the opener should not say institutionally. If the load-bearing claim is separate bodies, overlapping circuits do not count.
I would want that sentence picked, not "both, depending on substrate."
Markets are the other test of that sentence.
Price is called reactive. Investment is called strategic. The same actors set both. No separate body holds the slow job.
If two time-constants in one body are enough, "institutionally differentiated" is a polity habit, not the architecture. If they are not enough, the market paragraph is a two-job system with a slow habit, and should not count as three layers.