Hello David,
I have the same system on our boat except that I have a 100 Balmar alternator and a Balmar battery bank balancer.  I’m interested in how your problem is resolved and have a couple comments.    
To start I don’t monitor my alternator performance while underway.   But do monitor the battery system and solar performance at anchor.   
With this I’ve noticed a couple simple things.   The amount the system charges is based on how discharged the batteries are.    So for example I’d expect the alternator to charge at a greater rate after starting the engine then reduce a few minutes after.   Similarly our solar charging provides way more amperage to the house bank in the morning after a nights electrical use.   
I’m certain you know that our fancy external regulator controls charging to the batteries well beyond temperature.    
I use similar adjustments that you described for belt, temperature, and overall amperage output.    Even though I have both battery and alternator temperature indicators I don’t know how to determine if they are actively reducing the alternator output.  I just assume they are working properly.  It sounds like I need and additional gizmo in the system that provides more info. Or maybe look at our battery monitor while motoring…   
I’d also add that tension adjustment on the serpentine belt is difficult.   Too loose/too tight each has problems which can include overheating.   I’ve learned to be extremely fussy with belt tension and alignment.
Good luck resolving your problem and I’m hoping to learn more about our own system in the process.
Ray