For Bible quotations (e.g. from the Copy Bible Verses tool), follow the SBL Manual of Style and Christian Writers Manual of Style
Currently, Logos places a comma between the chapter:verse and the Bible version. Standard practice according to SBL and CWMS style manuals is as follows:
"For God so loved the world . . ." (John 3:16 KJV).
Notice the placement of the parenthetical note just before the final period, with no comma.
It would be really nice not to have to manually change this after pasting Bible quotations. Thank you for your consideration!

This can be accomplished by creating your own CBV style. Start with one that’s close to what you want (e.g., Quotation), then in the Style picker, click “Create a new style” at the bottom left. Delete the command from the =Footer section, then add a period and make other changes as desired.
For further assistance with this feature, please post on our community forums: https://community.logos.com/forums/141.aspx
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You can use [ShortPassageRef] for an abbreviated Bible book name. See the documentation for more: https://ref.ly/logosres/logos4help?hw=Copy+Bible+Verses
There is currently no way to write a CBV style to strip a trailing period from the Bible quotation (if the verse ends with a period).
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Joel Wingo commented
That's awesome, thank you Bradley. Do you know what commands I should enter to (1) omit the final period from the Bible quotation and (2) abbreviate the name of the Bible book in the reference?