I have limited experience on merchant accounts so I won't comment on that.
When you add an "empty" email account that's not linked to paypal you are basically just doing this so you can list. I think with newer ebay accts you will need to accept paypal until your merchant acct has been verified so this is so that you can sell before then. So this is only so that you can start to sell faster. If someone pays through paypal during that period the best thing to do is to email them to let them know you only accept payment through merchant account and have them cancel the paypal payment.
hope this helps.
good luck
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