Did you read the paper?
https://iopscience.iop.org/article/10.1088/1748-9326/aa6cd5/pdf
It's a pretty decent one but there are others that I find better done. I posted the world in numbers one because its got nice graphs and is well cited.
I'll post more if you would like to discuss it futher.
As for your question on nitrogen/phosphate runoff it's pretty simple. Organic fertilizers like manure take time to break down by microbial action into the exact same molecular chemicals as synthetic fertilizer. Say you have 4 months of production time when the plants can use nutrients. Microbial action on manure can take up to 6 months until it releases all of the nutrients. The excess nutrients that are release when no crop is growing runs off and causes environmental damage.
As for my comments on disease and seed, I can give you references to all of them except the SQMV. That's unpublished data that I used to convince some idiot C-suite types to release some capital investment. Gave a pathology tech a very bad few weeks one summer.
You are under the impression the all synthetic chemistry and GMO's are bad. This is flat out not true . They are technology that can be used for very f Good and stupid uses. Example a very good GMO is virus resistance (PRSV in Papayas). A fucking stupid one is Roundup resistance.