When I save files in MS Office applications, the 'save' function pops up with file explorer. Can I set Directory Opus up as the default?
No, there's no way to do that.
Is there a way to direct all 'save' options to show Opus?
No, sorry. There isn't a good way to do that in Windows that doesn't cause lots of problems. Especially not with Office which tends to use completely custom save/open dialogs.