Need to turn off highlighting coming from other Bible versions

It depends whether you attached the highlight to a reference or a text selection.

Attach it to a reference, effectively a bible milestone marker, and it will show in every bible, commentary, study bible that is indexed by bible milestone markers and contains that marker. And if you did not specify a notebook name the highlight / note will not have a place to belong and so will fall into the black hole called “no notebook” where everything that does not have a home resides and it is an all or nothing approach to hiding / displaying notes and highlights that fall into this black hole. Assign everything to a notebook name relevant to the reason why you are making the note / highlight and you will have much better control over the content you created and when you want to display it.

Attatch it to a text selection and this is where the corresponding notes and highlights option comes into play and adds another layer to the flexibility complexity that is Logos. And it needs to be this flexible complexity but as you have discovered is s little bit hard at first to figure out how it all works together.