Question: I want to start writing on an article that is probably going to be published in one of the IOP journals. There is a template for their publications, but it lacks some (for me) essential packages. Since I've never submitted an article myself, I want to be sure the editing process goes as smooth as possible by eliminating problems early. So here's the question:

Can I add all the packages I like to the template without pissing off the editor? I talk about things like `inputenc`, `fontenc`, `biblatex`, `microtype`, etc. Nothing fancy, but very basic LaTeX stuff. I also prefer to have a separate `.bib` file for my bibliography, since I have them already organized that way and do not want to manually copy the info into the bibliography as suggested in the template.

I already read the guidelines for authors and there was no mention of modifying the template, only that its use is highly appreciated. 

If anyone could provide any (preferrably inside info) on how editors work with submitted LaTeX files, that would help a lot! Thanks.

Answer: 
Unless explicitly forbidden, adding packages is usually ok and fully expected - e.g. in order to add support for listings, tables, symbols, encodings, operational utilities (extended macro/logic support), or specific features thereof. This should, however, never mean a general change in the appearance of the paper. Therefore, packages that globally alter fonts or font sizes are usually not allowed.

As for using a separate `.bib` file, you can usually work with that and (if explicitly requested by the guidelines - this varies a lot by publisher) copy the formatted information into the `.tex` file as late as for the camera-ready version (when nothing changes any more).
As someone who moonlights as a type-setter for a mathematical journal let me tell you something about bibliography.

Bibliography styles are different from one journal to another. There is nothing more terrible than having to reformat 60 entries by hand, and there aren't many things worse than having to reconstruct the .bib file in order to use the journal bibliography style more easily.

Sending the .bib file to the publisher is not a bad idea. If they can handle LaTeX, they can handle bibtex as well. I never worked with biblatex personally, so I can't quite tell you about that. But I do recommend that you submit you .bib file separately, and save the hassle to the type-setter.

Of course, this assumes that your .bib file wasn't hand-made. When you add an entry by hand, it has a high percentage of chance not being up to standards. Always use MathSciNet, if not then ZBMath, and if not, then Google Scholar as a last resort.