Exposed filter as Checkbox Radio Buttons has issues with Exposed Operator

I am having an issue with hiding the exposed filter when an Exposed Operator is used and BEF has a filter set with "Exposed filter as Checkbox Radio Buttons"

Steps to reproduce:

1. In views, set a field with options as exposed with "Exposed Operator" set.
   (In my case it is an entity reference field with "Render Views filters as select list" checked in the field settings)
2. Modify the BEF settings and set "Display "field_name" (Filter label: "Label Name") exposed filter as" to "Checkboxes/RadioButtons"

Expected:
When the Exposed Operator is set to "Empty" or "Not Empty", the exposed filter input should be hidden.

Result:
The exposed filter input is not hidden.

This issue seems to be the result of ctools' #dependency property not being able to find the exposed filter input because it is missing it's element #id

I have discovered the problem lies in theme_select_as_checkboxes() where the output element markup should contain the ID but it does not.

This issue may be more widespread with other theme functions, but this is the only scenario I am working with