As a long-time LaTeX user, I'm a little disappointed to read these results, but I fully believe them. I've spent countless hours fighting against the layout algorithm to get images to go in the right place, among other frustrating issues.

Efficiency aside, using LaTeX is expected in fields like physics and math, and if you write your paper in Word, readers will be biased against it (consciously or subconsciously). On the ArXiv, the vast majority of papers are typeset using LaTeX, and of the non-LaTeX papers, a large fraction of them are low-quality or written by cranks, hence the negative association.