Earlier this year, I needed to upload the LaTeX file and it needed to be written with the journal's template. In order to specifically fit into the journal's guidelines, the template was sent to some editing contractor where some minor changes where made to the source, e.g. "eq." to "Eq.".

As far as I know, a lot of the journals have their own automated build systems for the manuscripts to perfectly fit into their designs.

Nevertheless, I've also encountered PDF uploads. But even then, the PDF will be automatically checked for consistency.