Registering Excel on iPad, when iTunes and Microsoft account emails differ?
After days of looking, I've found the answer, via 
Having Problems Activating Office for iPad? Here’s a Simple Solution

Briefly:


Instead of saying “I already have a subscription”, choose the Read-only option
Then click on the Activate button at lower-left
Then you have an option to activate by using your Microsoft Office 365 account credentials


For me, doing this in Excel also activated my Word and PowerPoint iOS apps.