At this time the header spacing on our templates is fixed, so this isn't directly adjustable, but it does vary depending on the pre-defined theme used to create your theme. You might create a separate theme for the eBook version using the same fonts and settings, but experiment with different themes to see how the padding of each affects the ePub layout.
Then, you'll just have one extra click in the export process to select either your ePub theme or Print theme before exporting your file.