I don't think the mind itself is 'stratified', unless you're referring to traditional concepts...
I've actually found Panksepp's 3 "layers" to be incredibly helpful in my everyday life and--as noted--they align with my own experiences/intuitions.
(1) Primary affective
(2) Secondary classical conditioning
(3) Tertiary metacognitive & EF
I do think mind is stratified, and we can see this if we consider (1) Life as a whole, and (2) development and disease.
As Panksepp illustrates, if we accept evolution, then we accept that brains are stratified; if we accept that brains
generate minds (and that is the vernacular that Panksepp uses) then it follows that minds are stratified too.
Now, from the first person, phenomenological (tertiary) perspective, I don't think an organism will
perceive its mind to be stratified. That is, the mind won't subjectively feel stratified in a neurotypical organism. However, if one works with normally developing children or individuals who have had normal brain development and/or functioning impacted due to genetics, disease, or injury, one can see that the BrainMind is indeed stratified.
I also wonder if some phenomenologists or meditators might even be able to discern different layers of the mind. I don't consider myself advanced in either pursuit, but even I have intuitively felt that at times I am in a "primary" state of mind--pure affect for example or pure experience-- and other time in a "tertiary" state of mind wherein I'm reflecting on thoughts, feelings, or behaviors.
To reiterate, I don't think a neurotypical human would experience their mind as stratified; it has evolved over millions of years and a normally functioning brain should generate a normally functioning mind. However, by comparing human BrainMinds to our closest animal relatives, considering normal child development, and when normal development is thwarted, we can see the evolved, stratified layers of the BrainMind that typically work together seamlessly.