Logos stores notes in its own proprietary database, and I guess Accordance and E-Sword X do the same.
If there’s some option in either app’s notes to Reveal in Finder, there might be some hope to integrate with external tools, even if they will most surely not be based on markdown.
If as is the case with Logos, there’s some option to Copy a link to this note or something like this, there also might be some hope there to Hook-link a bible reference to an Obsidian note, as soon as Obsidian’s support for Hook links improves (I think the last release of Obsidian might help with that. People will probably discuss the improvements in this post.)