The new theming system is completely incompatible with customize theme. We believe the benefits outweigh the cons of not supporting customize theme. We will be updating our app with more and more options as time goes on to accommodate a wide range of customizations.
Pockets will still work on the Forum, but are not supported currently in the KB. Theme hooks still work as normal for the Forum, but are not supported in the KB. We’re moving away from that and towards a component configuration approach.
Foundation does have a default-master, with less code in it. We discourage modifying it for your theme. If you find we’re missing some pocket locations or a hook, please submit a feature requests. We would rather improve the product over all than to have customizations scattered across customer themes.
We do, however support custom JS in our theme editor.