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: 
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.
If these packages do not interfere with the paper layout than it is completely OK. However you should follow the instructions for authors style guidelines. For instance, if the template uses a specific package for generating tables, then you shouldn't change it. 
Regarding the bibliography I think that it is allowed to use bibtex and derivatives as long as the paper references style is preserved.