bioRxiv doesn't expose LateX files, they explicitly only use PDFs to make things easier. Which means you're going to need to reflow PDFs (a la https://docushow.com/), and I would guess there are a lot more edge cases there
Your solution using the LaTex source generates really nice HTML, congrats!
For now, it's hard to read: https://docushow.com/viewdoc?url=https%3A%2F%2Farxiv.org%2Fp...