We've run into some additional trouble that I think is related to this, thought I cannot see exactly how.
The first is going to be more of an issue for Design Tools, than for here. When we imported a course that had the incremented URLs I described above, the Design Tools widgets quit working, the error message indicated that they were not recognizing the pages as being in any modules. After changing the page names, so that the URLs would have a fresh name without sequence numbering, the scripts were able to recognize which modules the pages were in.
The issue that seems to be more on the Canvas end is that the top link on the left side menu failed to point to the imported Home page. Pages were selected for the Home Page and the course Front Page was also appropriately selected, but the link just loaded a blank page with the Home Page title. There wasn't a new empty page that had been automatically generated that was visible. When we selected a different page in the course as Front Page the link would correctly land there. Again, after changing the name and URL of our intended Home Page, the link loaded it. The imported Home Page title was the original and didn't have any version numbering.