Well my two cents.
I make my living Printing. I agree completely that you should first verify with the publisher/agent on format BEFORE submission for many reasons.
The biggest is this. Depending on their workflow can either make things run smoothly or cause a nightmare for the printer. The reason why many publishers/agents request .doc is not really for the editing/changes features but rather that the Printer (publisher) will use the files to import the raw data for impostitioning to a final piece for running on the press. They usually request certain fonts and sizes so that their automated impostition “flags” these and changes these on the fly to the Book (final piece) settings. Such as 12 pt courier being converted to 10 point Times RomanPS etc.etc.etc.
Not all shops (printers/publishers) are the same and have different software and workflows. Some can extract the data right from a PDF where others are setup to use .doc only.
Some shops want their PDFs set to a certain size and output setting (PDFs are all not the same) once again it all depends on on the Printer/Publisher and the final job they are printing. They ay impostition the final PDFs but they better be exact to size and settings or the impositioning could be thrown off screwing up the job and delaying things and costing more.
So ask and make sure BEFORE submitting because if it is the wrong format and you convert to another format late in the editing approval stages then misprints or delays could occur because everything would have to be reproofed and approved before they put it on the press.
A rule of thumb I would advise is this. Anytime you are setting up something that someone else is going to print TALK to them and find out exactly how they want things before you do ANYTHING.
A prime example is when people have pictures (raster) they wish to print. They usually bring in something that the resolution is too low or already screened (been printed before). This is a nightmare. Or they have ungodly high resolution pictures that delay the printing
People ask “Well what resolution should I scan or take my pictures at?” It varies but here is how you find out.
It is a simple equation.
Final Resolution (PPI or as most call it now DPI) = 2 X the line screen (LPI) of the output device at Final size. or simply put
DPI=2XLPI@ Final Size
Now you need to find out the LPI from your Printer/Publisher (If you can’t find this out you can use the scale below)
Most newspapers and Fiction books are printed at
85 - 133 LPI (use 133 if unsure)
Most standard magazines and commercial Printers print at
133- 150 LPI (use 150 if unsure)
Most high end digital prints and high end art catalogs and magazines print at
175 -210 LPI (use 200 if unsure)
The most common of all is 150 LPI so if you have no clue use 150 LPI
So a picture that is 4x6 and its final size will be 4x6 and our LPI is 150 the equation looks like this
DPI = 2x150 = 300 DPI I need to scan at or set the resolution to when the picture is 4x6"
Now if you need to enlarge the picture there is one extra step
Let us say the actual picture is 2x3 but we need to enlarge it to 4x6 for printing. We find out how much we need to enlarge it by in a percentage. Which would be 200%
So now the formula is
DPI=(2 X LPI) x Percent (which is 2.0)
So now we have a 2x3 color picture we need to scan for printing and it will be 4x6 when printed. We are printing 150 Line Screen (LPI) so the formula comes out to this.
DPI= (2 X 150) x 2.0
DPI= 300 x 2.0
DPI= 600
Crazy huh? Now imagine when I do a catalog that has 800 photos. 
If all else fails use 300 DPI at a size that is close or slightly LARGER than the final piece and you will be OK.
That is how you get really NICE pictures printed by following that formula.
Why did I go through this long and exausting explaination. Simple.
Most people just bring in Photos that are already scanned and set in resolution BEFORE asking the printer/publsiher what the specs or requirements were.
SO then we have to go thorugh each picture and “adjust” them which takes more time, costs the client a lot more money and delays the due date of the final printed piece.
That is because most people do not know the complexities of printing.
Now your publisher is a printer. That is the most costly overhead is actually printing.
Play it safe and ask for something (Spec sheet whatever) that lists EXACTLY how they want the document submitted. That will save much time during and after the approval process. Believe me Much time.
