It looks like Transport Gateway 3.5 web gui removed the ability to configure the HTTP and/or HTTPS ports used by the TG.
Is there a way to manually configure that instead?
No, version 3.5 only works on ports 80/443. Please continue to use version 3.3 if you require the TG to listen on an alternate port.
Look for Transport Gateway 4.0 on the download site. 4.0 has the Web GUI and also allows the HTTP(S) ports to be changed.
Just be aware that changing the HTTP port will also impact the Web GUI. Once the port change is saved, re-enter the URL for the GUI with the new port number.