In my past experiences, I have almost never typeset my manuscripts according to the formats required by the journals to which I would like to submit. I leave my manuscripts as produced by the LaTeX article documentclass.
Recently I am wondering: Would such a behavior generally give handling editors a negative first impression?
Answer
Speaking as both an editor and reviewer, I am definitely prejudiced against a paper that fails to follow prescribed submission formatting (which may or may not relate to the final published format). It is simply a matter of professionalism and prior correlation.
As an editor and reviewer, you see a wide range of material submitted. Some is really good, and some is really bad. I've even gotten a few that were outright insane. The vast majority of the papers that failed to follow prescribed formatting were definitely not good.
Making a good-faith effort to follow formatting requirements generally isn't hard to do, and especially when doing so just means using the journal's LaTeX package rather than the default. Neglecting it means that the author is being sloppy and unprofessional at something easy. This doesn't necessarily impugn their science, but if they don't care enough to follow professional standards on something easy, it's a good indicator that they are likely to be unprofessional in other places where it matters more as well.
One exception: I am likely to give a pass to particularly aged/emeritus types who have a solid track record but are clearly not comfortable with modern word processing technology.
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