First, to be clearer about terminology: in Marketo, the email address is not actually a unique identifier. Not only is it not mandatory (in database terms, that means that all the leads with a blank email address in fact have the same email address) but, as you know, there's far from end-to-end protection against duplicate emails. Email is merely the default deduplication key when using certain (but not all) Marketo functions. Custom settings exist so that some functions use the email address + one other field as the dedupe key instead, but that still doesn't make it a unique id, and still, not all functions will use the custom dedupe key.
The only guaranteed unique identifiers in Marketo are the Lead ID, Unique Code, and Unique Name. Other fields might be treated (by some functions and outside apps) as if they are unique, but Marketo will not ensure uniqueness. An example is when you sync an outside system to Marketo that has a special guaranteed-unique field associated with each of its records. As long as Marketo settings and flows are careful to never touch that field, it'll stay unique in Marketo as well. But it can still be changed within Marketo and the system won't blink.
Anyway, to your question: the Marketo feature that stops the same batch flow step from sending to the same email address more than once isn't deduplication per se. It's a special feature to stop spam-like behavior, and isn't related to create/update deduping. To work around this feature, have your Batch Smart Campaign call Request Campaign on a related Trigger SC. Everyone who qualifies for the Batch SC will then get the email, since the email step is standalone.
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