lexcyn - glad you got this sorted out, and thank you SeitzM for playing support agent here on Microsoft's behalf :).
We are working on an improvement to allow you to more easily add your Microsoft 365 subscription that is purchased with a non-Microsoft email address.
I tried this out and added my main MSA that is attached to my M365 subscription as the "primary" account, but still no good. I think this is the issue for me since my primary account is through Gmail:
You guessed this correctly. When you added your Gmail account to Outlook for Windows, you connected Outlook to the mailbox and calendar on Google's servers, with your Google email and password. You didn't log into your Microsoft account. So Outlook didn't know about your subscription at all. Once you added the alias to the account, then we were able to properly read the license.
But in the future, we'll allow you to just log into you Microsoft account directly to get the license, even if there isn't an Outlook.com email address attached to it.