This actually isn't entirely MS Office's fault. I used to do technical support for Adobe Acrobat, and a very common support call was, "My document looks fine on the screen and prints to my printer fine, but when I make a PDF the layout is messed up!"
MS Office formats the page relative to the currently selected printer's printable area. The problem arises when you have a document that puts objects near the page margins, and then change the selected printer (File > Print > Change printer and click "Close" instead of "Print"), MS Word reflows (reformats) the document on-the-fly for the new printer.
If your template is well-designed, nothing major will change (maybe some line breaks). A badly designed template, like one that uses manually inserted page breaks instead of letting a style insert the page break, will break in interesting ways, like inserting an unnecessary blank page or floating text next to a table or something like that.
Nasty reflow almost always boils down to poorly written documents that do stupid things like use an empty paragraph to put a blank line between paragraphs, use underscores instead of underlined spaces to create a blank, use a manual page break instead of a paragraph rule to force pagination, and other hacks. Learn how to use the software, and it'll behave properly.