I don't see why a custom should be any worse than an off the shelf 'JDM' exhaust system if it a) has sound workmanship and b) the materials are fit for purpose.
Generally the off the shelf packets have a bit more RnD with regards to the muffler, so as long as you're using a good muffler, you'll be fine.
Plus, a shop may or may be easier to communicate with with regards to warranty and reworks
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