so many things wrong about this post... Where to begin... Why do you ask a question if you seem to already have a answer? No it is not just "in the head". Think further than just the usual argument of a longer stem travels a greater distance when rotated a certain degree when compared to a shorter stem. Think weight distribution, body segment placement... A scrunched up upper body will react differently than a stretched out one when given a stimulus.
Yes a human can feel the difference between a flexy and stiff stem. Period.
Muscle groups does not equal muscles. Your body recruited wayyy more than 6 muscles throughout a pedal stroke. Try somewhere around 40 to 50.
Pedaling a bike does not necessarily make your body rock. Coordinated movements of the upper and lower body can counteract the bikes/body "urge" to rock back and forth. You don't see froomy rockin all over the place with that crazy cadence
How you combine those assumptions to draw the conclusion that it is somehow related or more noticeable than stem deflection I have no idea. Maybe I'm missing something here.
People like different setups for difference applications. Maybe some people prefer a stem that is somewhat soft. That's great. But there is definitely a noticeable difference between short/long stems and soft/stiff stems. How an individual connects with their bike is very important.
One thing I have learned over the past couple years is that lab results/numbers don't necessarily correlate directly with real world experiences and conditions. There are many factors that influence a sensation or outcome. It's more than just deflection.