If I understood correctly, your internal website is running on custom ports like 8080, in such a case, you can use because when you setup internal URL, you can include ports as well.
Intenal URL - http://mywebsite:8080/
It should just work fine.
This browser is no longer supported.
Upgrade to Microsoft Edge to take advantage of the latest features, security updates, and technical support.
May I use non-80 and 443 ports for Azure Active Directory's Application Proxy
If I understood correctly, your internal website is running on custom ports like 8080, in such a case, you can use because when you setup internal URL, you can include ports as well.
Intenal URL - http://mywebsite:8080/
It should just work fine.
You can change or use any available for your internal application while specifying internal URL, however, for Azure AD app proxy service you cannot make changes to ports it requires to communicate.
Azure AD Application Proxy connectors connect to Azure via HTTPS (TCP Port 443) and HTTP (TCP Port 80).
Open the following ports to outbound traffic.
80 Downloading certificate revocation lists (CRLs) while validating the TLS/SSL certificate
443 All outbound communication with the Application Proxy service
Please let me know if this help !