Actually, my single-portfolio.php is exactly the same as Generatepress single.php. I just made a child version to make future customization…
My pageheader is set as “Above content area”, but the other option has no positive effect either. I still think this is an interesting bug for you to dive in and make your awesome Generatepress even better compatible with this kind of usage.
Is there anyway I could PM you my wp login so you can see for yourself how I managed to find this bug?
[Edit]
Yup, it definitely a bug in Generatepress, I just came to the idea to change my portfolio post-type to a normal post-type. It gives the same lay-out problem as mentioned earlier. I think it had something to do with a wrongly placed ‘generate_after’ code versus the the way I prefer to use Generatepress: merged and transparant headers on all pages. (Home, pages and posts). It has nothing to do with a custom post type, thats for sure now.