If a publisher accepts LaTeX manuscripts they likely use LaTeX also for the final type-setting. I am sure there are exceptions but could not point you to one.
The benefits, apart from obvious LaTeX benefits such as equations and built in standards for references, numbering of equations, figures and tables etc., lie in the way a manuscript can easily be taken from a manuscript form to a finished product.
Many journals have class files that allow you to move from manuscript to essentially "proof" mode by changing a switch in the document and "re-compiling" it. This also means that the journal can go to typesetting without moving file contents to a new format or another program (not many journals are type-set in Word).
In the case of journals that do not have class files for use by the author, moving a manuscript from a generic LaTeX format into a specified journal format is not necessarily difficult. There are probably many different approaches to this but from a LaTeX point of view all definitions of a document are there in the plain LaTeX file and it would be easy to apply a class that re-defines the plain format to something that will yield a finished layout.
With LaTeX focus is on writing the text, not formatting the manuscript. As Editor-in-Chief for a journal that uses both Word and LaTeX, I have spent many hours weeping over hopeless Word formatting (including field codes that do not work) that is both unnecessary and complicating moving the document to the type-setter. LaTeX is a text file and so does not contain anything that cannot be easily spotted and changed if need be.
So, to be fair, one can mess up with LaTeX as well, and I want to point at an overarching rule which is to always strictly adhere to any instructions for authors provided by the journal and not to send in material that is of a format that differs from what is asked for.
So the benefits of LaTeX is that the move from manuscript form to finished layout is simplified and reduces the amount of manual work for the type-setter. But, in all type-setting there is always need for manual control so LaTeX is not 100% automatic, just closer to it.
About BibTeX referencing: Most journals and I would guess type-setters want the manuscript in as few parts as possible. therefore many provide a
.bst for the reference style but ask that you run BibTeX to produce the
.bbl file (containing all references properly formatted with
\bibitem formatting) and then paste the content into the document to provide a complete and correctly formatted reference list inside the document file itself.