Hi there,
Currently whichever Header Element was registered first gets priority over any subsequent headers that have the same display rules. Hence the need to use the Exclude rules to avoid conflicts.
If you are requiring different Header Elements by Post Type then i would not use the Entire Site Rule. Instead just create one for each type. This reduces / removes the need of the Exclude rules and removes conflicts.
I have not noticed the ‘bug’ relating to the image uploads. Maybe a cache or plugin conflict issue?