There are a lot of rules about writing which are subjective. Things can be broken as long as it's broken well, in the right ways, and even then the recommendation is to avoid doing so at all costs.
When presenting a manuscript to an agent, the rules are less flexible. There are certain expectations that have to be upheld.
That being said, always default to what the agent is asking for. If they want your manuscript font in pink, 14 point, comic sans, then that's the way you should submit your pages. Each agent/publisher is going to have slightly different preferences, and if you can't follow simple directions like those, there's a change they may not even read your query.
That's not a guarantee, but why wouldn't you take the chance to make the best impression that you can? Especially if the agent you're querying is in your top tier.
Based on my research (and while I have done a fair amount I would recommend doing your own before you start querying), the universal submission manuscript looks like this:
12pt font (in black)
Left-justified alignment
Times New Roman (or sometimes Arial)
If you right click over the Normal Style at the top of the page, a drop down menu will appear. Click on Modify to change the default text settings for the entire document.
Double spaced
1/2" indent on each new line (don't use tab to indent but set in paragraph settings)
In Word, click the arrow in the bottom right of the Paragraph box. This will take you to the pop up to format your paragraphs for the whole document. You want "First Line 0.5"" under the Indentation section, and "Double" under the Spacing section.
New chapters beginning halfway down a new page (read page breaks)
In word, the command is simply Ctrl + Enter.
Standard 8.5x11 pages with 1" margins
Number your pages from the first page of the story rather than the title page
A title page with your name, address, and contact info
Also, your title, by-line, and word count centered on the page
You want your story to stand out for it's content, not its appearance. Manuscripts that are all formatted the same way make it easy for agents to read, make notes, and swap from one book to the next. If every book looked different, you can imagine how that small change and readjustment might slow down a process.
Agents go through thousands of queries in very short amounts of time. Many have processes to cut down on the pile as quickly as possible and one of the easiest ways to do that is by looking at submissions that are clearly different than what they asked for.
Now, this is what your polished manuscript should look like, but that doesn't mean you have to write the book in this format. You can write in whatever way is comfortable for you whether that's an Alphasmart, Word with 20pt font, or Pages. If you find scripts get the words flowing, than use it.
But before you send it out make sure that the whole document is formatted in the way the agent wants it.
This is said over and over as well, but make sure that your story is as polished and sparkly as it can possibly be. I also recommend making sure that someone reads your final draft. Even if you only make two changes, get someone to read those changes to check for typos, consistency, pacing, etc.
It also needs to be finished (unless you're querying non-fiction). Agents won't accept half-completed fiction books. They don't have time to help nurture a story to completion--and that's not their job. Yes, some agents do help with editing, but they don't help you write your story.