[cozzyd]

You typically send a .tar.gz of tex files (and, figures, .bbl, etc.) to the journal. And then you typically upload something very similar to the arxiv (I have an arxivify Makefile target for for my papers that handles some arxiv idiosyncrasies like requiring all figures to be in the same folder as the .tex file, and it also clears all the comments; sometimes you can find amusing things in source file comments for some papers).

Some fields may use Word files, but in most of physics you would get laughed at...

It is true that most journals will typically reformat your .tex in a different way than is displayed on the arXiv.