I inadvertently found a way to trick it that seems to work perfectly. I was cutting and pasting the "did you mean suggestion to see if it worked and accidently pasted in the "?.com? at the end. Entering "https://siteURL:9999?.com?" strangely allows the site to be saved and it it is correctly shown as "https://siteURL:9999" in the list. I think Google is assuming the ? mark is part of an unnecessary HttpGET string and truncates it leaving you with the correct URL.