41 foot pounds of torque on those socket head cap screws, to me, is seeming to be close to stripping the threads out of the aluminum.
If you have enough grip length then 41 is fine. Thread and bolt material is only one of the factors that determines whether or not a combination can handle a given torque.
I haven't taken a torque wrench to those but knowing how notorious, torque wrenches are for being out of calibration, it would be a good thing to have some moly's standing by in order to be able to fix the ripped out threads you surely will have.
Torque wrenches (if treated properly) are no more prone to going out of cal than anything else.
The first time, at the original manufacturing date it may be a proper torque value (41 ft-lb), but subsequent loosening and tightening exercises will adversely affect the threads inside the aluminum and in my opinion will cause the threads to eventually strip out.
Again, if you have enough grip length then the specified torque can be applied hundreds of times with no damage to the threads. What you're suggesting is that after the first installation you should reduce torque? Okay, to what value? Half? Two thirds? And do you keep reducing it every time you run a torque cycle on it? Do you realize how ridiculous what you're suggesting is?
Secondly, the socket head cap screws are tightening down the top bridge which in turn is holding the handlebars, so anything gained by an extra few degrees of turning the screws to attain the noted torque value will gain very little in the force being applied directly to the handlebars but greatly increase the possibility of a failure of the threads in the risers.
Wrong.
Lastly, and equally important in the discussion question is the introduction of lubrication of the threads with something such as an anti-seize compound. Lubrication will absolutely alter the torque specifications and could also be a reason to be more cautious when applying the stated torque values.
Might be the only correct thing in all of this. Lubricating fasteners does require that you take it into account UNLESS the manual states that the fastener is to be lubricated or coated with anti-seize. Then the value is factored into the torque in which case if you do NOT lube it you're probably under torquing it if you use the specified torque values.
Steel nuts which are generally grade eight or greater and steel threads have a greater ability to withstand over-torquing. Aluminum does not posses the same ability and assuming you can stretch a grade eight socket head cap screw which is threaded into aluminum threads, to me, is dangerous ground.
Steel fasteners of any ilk (nut, bolt) are NOT generally grade 8 or higher. Grade 8 is expensive and only used where strictly necessary. And I don't see where anyone said you can "assume" you can stretch a grade 8 socket head cap screw.