I've managed to upload external ePubs to Kobo's Desktop App on a Mac. Whether a similar process would work on a Windows machine, I can't comment, but in case this helps any Mac users out there:
You need to create a new folder in your user's Documents folder called Digital Editions.
Copy the ePub file into this folder.
Don't hit the sync button, that won't ...
I found a hacky solution to the problem by editing the eBook's styling using Calibre.
Importing the ebook and then right click on Edit book which opens the actual contents of the book. Now the actual formatting is done via a stylesheet (in my case called stylesheet.css).
In this stylesheet there are the generated properties for the image sizes, e.g.