It sounds like you already know the answer.
Hand soldering is much more stressful to a board than mass soldering, because: * It is more localized and there is no preheat. * It is more difficult to control. [Different connections require different heat times, but these estimates of time are difficult to judge [a poor estimate requires retouching]. And operators try too keep their iron as hot as possible to increase their throughput. Hot iron use puts a higher thermal shock on via and pad adhesion.] * And on and on ...
This thermal shock, no preheat is a problem because the different materials the comprise the board [eg, epoxy, copper, glass fiber, etc] have different rates of expansion when heated. Remember that eperiment that your teacher did in high science class when he heated a bimetalic strip and it bent? That's exactly what's happening to the materials in your board.
The intermetalic layer grows as a function of time and temperature above zero degree Kelvin.
Finally, going back to your original point "I have insisted if it looks good don't touch it." That's the real issue. You and your operators have different standards. [Can you imagine how much touch-up your going to have when you go to leadfree?]
Continuing, many years ago, we were touching virtually every board. Our operators were "painting" solder over blow holes that were caused by out-gassing of moisture in the board through the barrel of through holes. There was nothing good going on there. So, we worked with our suppliers to inprove in-bound materials and improved the storage and work environments. Our operators were doing the best with what they had. There was a problem that the operators saw, but others needed to see in order to improve the situation.
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