It is a tricky one. Personally I don't take much stock in published EPC's for the reasons you mentioned. Instead I speak to the account manager and ask what the EPC is from say the PPC affiliates. This then gives me an understanding of what can be achieved via my chosen method of promotion.
However I've voted yes as it can give you a very general guideline. And if for instance you notice a high EPC for a merchant that you hadn't considered promoting before, then it may give you a reason to give them a push.
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