Sam, like Dan we primarily store our emails locally and do everything through standard programs, not email send programs. I've had some issues with email programs in the past, but I believe that one of the reasons they have not been able to link design studio emails to email programs is due to a reporting limitation.
In short, Marketo will only report on the send, open, and click of an email asset a single time. What that means, is that if you send the same email to the same person twice, your email performance reporting metrics (not necessarily your send flow metrics, but reporting on these is not always your best bet) will only register the first send of an email, the first open of the email, and the first time someone clicks on that email. An example of this being problematic if you use the same asset in a monthly campaign, and only look at an email performance report for the month. If you sent the same exact asset last month, it will only show the new people (didn't receive it last month) in this month's report. But, if someone was sent the email last month and this month, didn't open the email last month and they open it this month, then they're recorded in this month's open metrics on that email performance report. Marketo wants to avoid this in their native reporting of email programs -- which is why they require the assets to be made new for each email program.
I would hope that in the future, if they're able to get past this reporting limitation, that they would be able to have global assets used in email send programs. Until then, I don't see it happening.