[WanderPanda]

It needs to be intact, the pdf is rendered by the arxiv backend based on the source

[semi-extrinsic]

You can upload only the PDF on ArXiv. Useful when you for some reason (e.g. client request) publish in certain engineering conferences that only allow Word submissions...

[cozzyd]

if arxiv detects that it's a latex-generated PDF, it will reject it. Though it's probably possible to launder the latex-generated PDF through ghostscript or something to evade detection (I haven't tried...)