I really appreciate your input, @lizardmenfromspace. It was my hope that other people from the PKM community would find it an interesting case study.
On headers and readability: With a bit of rudimentary CSS tweaking1 , I was able to create a reading experience that is totally fine for me.
I do love though that in your approach you can quickly see the verses you already have other notes on. Until there is an indication for linked headings, it is hard to see on which verses you might have notes on. Having a consolidated “Commentary” section on each verse is also very helpful.
I definitely see the benefits of this approach, I am just hesitant to go through the effort of importing and formatting the Bible again 
How did you create the superscripted verse numbers? Did you format them manually/via regrex or were you able to copy and paste the format?
This system also introduces just a tiny bit more friction for a new reference. Currently, typing [[Eph-1#8]] does the job. In the other approach after creating a new [[Ephesians 1.8]] reference, I would have to go back to the paragraph to add that link, right?
Again, thanks for your input. I can really see the benefits of this approach and I am on the fence of changing my whole system. 
1: In case it is helpful to someone, here is the code. If someone would be willing to help me out in how to get rid of the space after each verse, I would really appreciate it!
.markdown-preview-view h6
{
position: relative;
left: -3%;
top: 26px;
line-height: 0px;
margin-top: -20px;
margin-right: 3px;
font-family: var(--font-family-preview);
font-weight: 500;
font-size: 10px;
font-weight: bold;
color: var(--text-faint) !important;
}