I know there is the "Corresponding Notes and Highlights" Feature for Interlinear-enabled versions and that it is not yet (re-)implemented for Logos 8. For one, here is my vote to prioritise this!
Apart from that i think it should go further than that. If i highlight and add note to a text within a verse (because that is what you usually do - you highlight content, not necessarily full verses) - i would want this note to be referenced also in other versions. I know that you can't match the text if it's not interlinear. however the note will most likely also be relevant in another bible version. Especially in the context of a software like Logos where you happen to work with a lot of versions, i think it would make sense to give access to notes from all versions. For example this could be integrate in the (upcoming) "Corresponding Notes and Highlights" feature: when a highlight/note can't be matched via interlinear, it is attached as an (special) icon to the verse number.
Additionally i would also like to have references within the note text to show up at that corresponding verse. Maybe also with a special icon (via optional visual filter) that indicates the reference/note beside the verse number.