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There's no harm at all if the Reply-To domain is all you're talking about. The vast majority of Marketo customers have Reply-To: @ their main domain, and that domain receives mail via their corporate mailserver, also an "alternate server."
If, on the other hand, you have branded sender domains on your account (an additional cost) and you're talking about the *SMTP envelope sender* not simply the Reply-To, then Marketo will not be able to process out-of-band bounces, as they will go to ExactTarget. That ain't so good.