Must be significant, otherwise both would not have their own project templates.
I am asking this because I want to use Scrivener to write a trilogy and don’t know in which project templates I should start. 
I’m not aware of much difference. The Parts template starts with the assumption that you will gather several chapters into a Part of a book, and then the next set in another Part, and so-on. It assumes you’ll make a folder for each part, and indented under that, a chapter folder for each chapter, and indented under that, a few scene documents. It will automatically add “PART ONE” and “PART TWO” to each part folder’s title during compile, and likewise will do that for chapter folders.
It’s easy enough to transform non-part binder structure and create part folders, then when you compile, start by choosing the “Novel with Parts” compile preset. The opposite transformation, where you move your chapters out of Part folders and choose the non-parts “Novel” compile preset is similarly easy.
If you know ahead of time how you want to structure your book, then you might as well start with the appropriate template, but otherwise, I wouldn’t worry overly much about it. In fact, when I start a big project, I rarely even think in terms of chapters, but just brainstorm on a cork board, adding and rearranging story ideas as I build out a plot. Only when I’m about to start writing, or when I’m done with the first draft, do I bother to group or split up documents into chapters.
In short, start however you like, and don’t worry too much about the end product until you’re at the end of producing it.
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Interesting, thanks for your advice.