Here is the product team's official stance on this:
For pre-fill to work on embedded forms, it requires a publicly accessible API that retrieves lead information, which can include personally identifiable information such as email addresses, mailing addresses, names, and phone numbers. For us to make enable pre-fill on embedded forms in a responsible manner, we need to make certain that the API is created in such a way that it’s acceptably protected from brute force attacks that could allow an attacker to retrieve information about all leads by guessing Marketo cookie values, as well as making certain that the API doesn’t expose leads to XSS (cross-site script) attacks that could be used by an attacker to steal a lead’s info when they visit the attacker’s site. These issues doesn't exist when the form is on a Marketo landing page because we process the content of the page on our servers and there is no API exposed publicly.
This is 100% on our roadmap and we know how much customers would like this...it just requires a very thorough review by our internal security team. I plan to work on this next year.