Hi @J Tech 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:
-You had a web app and need it to resolve the hostname of an Azure server but your Web App could resolve the hostname
-You had the DNS server listed in the VNet that resolve with the FQDN but I wanted the short name to also resolve.
Solution:
-You were able to get the web app to resolve the short name by adding a hybrid connection which resolved your issue.
Thank you again for sharing the solution that worked for you.
Best,
Grace