When Command+Tilde is pressed, Inkscape windows should navigate forward. When the Shift modifier is added, then Inkscape windows should navigate backward.

What is forward and backward in this context?

Note that this is a user forum, not the place to report bugs. If you find a bug, please fill in a report at https://inkscape.org/report (you can also search if someone has reported the same thing already there).

Is that navigating your file manager?  Or navigating Inkscape's Open dialog?

Have you made the proper changes that are needed for all the key shortcuts to work in Macs?  Command and Alt keys need special attention:  https://inkscape.org/learn/faq/#mac-os-x-specific-issues

The linked FAQ item is valid only for 0.92.x, not for 1.0beta (or 1.0).