It depends to your needs. If you want to be accurate you need to use different entries because there are different ISBN's. This is also the case if a book is a modified version e.g. error corrections, actualized version/edition. For metadata queries and bibliophile view you like also to archive different ISBN's to different records. In the end different ISBN's are different books in the real world.
On the other side, it is "only" a format issue and you are doing this for your personal hobby. You can use e.g. Book details to add all different format ISBN's to the same record. As long as you don't update the metadata of the book format in the library they will stick with the original information. This is why I don't like the idea of some users to update format files automatically in general with changed metadata from calibre records (what is fortunately not the case).
So, in the end it's a personal decision how you want to use your library
