For example, increased testosterone levels correspond to increased stress tolerance. The testosterone levels increase in man and woman up to age of 35-40 years.
So if you just sit and do nothing, your body could work in favor of your mind, if you're young enough. Chances are you were.
But if I'm reading you correctly, you seem to imply that all the benefits mentioned could be explained away by age-related hormonal changes. I find that hard to believe based on the strong correlation I experience between active meditation practice and greatly increased mental ability. It is particularly noteworthy that I'm able to observe a clear decline in my capability to stay equanimous and focused whenever I have had longer periods away from practice, which should not be the case if we were dealing with mere age-related endocrine changes.
Short time effects like "staying focused" could or could not be explained by that. I think I have just too little data to explain them at all. All I can do is to speculate.
So I begin speculating.
Let's say that by meditation you try to calm your mind. You lower your stress hormone, cortisol. By doing that you elevate your testosterone level.
http://www.ehow.com/about_5162836_effects-cortisol-testoster...
Does that mechanics explain meditation effects?
Myself, I prefer to walk a forty minutes or longer to boost my mind next day and to lift (pretty heavy - 160+ kg) weights for testosterone.
Both activities are scientifically proven to help mind. Aerobic exercise provides brain boosting: http://www.hnsearch.com/search#request/all&q=aerobic+exe... Weight lifting increases self control: http://www.nytimes.com/2010/01/26/health/research/26exer.htm...
I think I should write a presentation about all that.
That said, mounting scientific evidence indicates that meditation also changes our brain structure in ways that have AFAIK not been observed with exercise.
For me my own experience would seem to confirm this. The benefits I observe from meditation are both qualitatively and quantitatively different from what I gain from exercise (both aerobic and heavy weights).
Experienced meditation practicioners can fire almost all neurons in their brains. In MRT it looks like epileptical seizure.
So I stay on the "don't meditate, you'll be safer" side.
That said, I find your caution perhaps unwarranted. Many other circumstances are known to cause changes in brain-structure, e.g. growing up bilingual, but I think it would be rather unwarranted to warn against childhood language learning on the basis of this.
Personally I am content with the proof of my own experience; the changes I see in my own psyche and mental performance are entirely positive.