We have many of Marketo forms on our main domain (not on Marketo LP) and all of them are currently working with pre-fill. So, I decided to do the same when I started building the subscription center. Interestingly, the pre-fill doesn't work on this subscription page, though I copied most of the codes from the page where the pre-fill is working.
On the form, "are you a customer" checkbox on the very top and the country picklist at the bottom should be pre-filled, because these fields control visibility of some fields. And, the On/Off on each content type needs to reflect whatever the visitor has requested before (or the manual change from the backend). For Now, when I fill out any form and thus cookie myself and go to the subscription center, it shows On on all the items though even if I changed it and came back to the page.
The subscription center page is here - Email Settings