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DC question
You are misunderstand "set_dont_touch" with "set_dont_use".
"set_dont_touch" is some hard mirco or clock you don't want synthesis tool to change it.
"set_dont_use" is not to use certain cells.
You have to put clock skew into your mind in order to understand what is Hold time violation. Your data path may be shorter than your clock skew to make hold time violation happens.
Uou can use Verplex to compare the netlist before and after layout, if no error found a STA pass would be goo enough, but make sure your constraint file is good enough including chip boundary.
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