The SMTP server is a free-form text-entry field, but the port field I can only select port 25 or 587; I’d like to be able to enter any number between 1 and 65535 (which is the valid range of TCP port numbers).
As it is right now, I cannot use the SMTP feature since I am using a non-standard SMTP port.
That is the correct conclusion. You should use one of the standard ports. Manager nor most other applications would you allow non standard ports, especially for SMTP because of spammers, fishing emails, etc. So it is excellent that Manager adheres to standards. You can always just select print and save as file and use your email package with whatever port is suitable to you.
Respectfully, Manager is not running a server, it is contacting a server and in my case, on a nonstandard port. My laptop does not connect to any mail server directly, but through a ssh port forward to my mail server. There are many situations where the computer running Manager may not be able to connect to a standard SMTP server (residential internet where the ISP blocks anything but their own mail server, for example, or working remotely, etc.).
Restricting the port that Manager connects to does not increase security, it only limits functionality.