This is not really a problem with the header only, this is affecting all the checkbox type fields that have default="0" such as the Coming Soon, Preloader, Boxed Layout, Custom Font, Blog Details -> Disable Modules fields, which are the ones that have dependent fields that are not loaded, there are other individual checkbox type fields that are loaded and have default="0" because when I activated boxed layout it has no effect.
If it is confirmed that it affects all the checkbox type fields, it is not a problem from the templates but with the type of field in the Helixultimate Plugin (if it is a Helix field) or with Joomla which affects all the default="0" of the field types or the checkbox type.
This is my first review, I have not yet reviewed the Helix code and even less the modifications of Joomla 5.2.4
Regards