arXiv accepts various flavors of TeX, or PDFs not produced by TeX [0], and automatically produces PDFs and HTML where possible (e.g. if TeX is submitted). In the case of the example paper under discussion, the authors submitted TeX with PDF figures [1], and the PDF version of the paper was produced by arXiv. The formatting was mainly set by using REVTeX, which is a set of macros for LaTeX intended for American Physical Society journals.

[0] https://info.arxiv.org/help/submit/index.html#formats-for-te... [1] https://arxiv.org/format/2312.12451