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We will have to defer exploring whether Marketo templates will allow us to a) import our designed HTML without b) removing style tags from the body (for the benefit of media queries), until next week. Thank you all for the suggestions. The client I'm observing this in is Parallels/Horde, Courtney, but that's not the issue. Standards aren't laws. There should be an expert mode. Thank you!
Not sure if this was ever resolved since it was a few months ago, but in order to get MSO conditional tags to work and render, they must be placed in an editable region on the email level. They can not live in the template or Marketo will strip them out upon save. Additionally there has been an update on the platform that now allows conditional statements, I have not tested to see if statements can now reside in a template.