I'm glad that you were able to resolve your issue and thank you for posting your solution so that others experiencing the same thing can easily reference this! Since the Microsoft Q&A community has a policy that "The question author cannot accept their own answer. They can only accept answers by others ", I'll repost your solution in case you'd like to "Accept " the answer.
Issue: I have other AFDs setups with a single endpoint and multiple routes for a multi-tenant environment that works fine. Is the problem the two endpoints with different routes?
Solution: Unlike CDN, AFD requires the custom domain to also be added to the storage account.
Go to your Storage account, under Security + Networking select Networking. Then in the center menu select Custom domain, enter your domain name, and select "Use indirect CNAME validation". You'll need a CNAME record for this to work. asverify.customdomainname -> asverify.storagename.blob.core.windows.net
If you have any other questions or are still running into more issues, please let me know. Thank you again for your time and patience throughout this issue.
Please remember to "Accept Answer" if any answer/reply helped, so that others in the community facing similar issues can easily find the solution.