There is an issue with Command ships becoming available when the requisite technology has been researched.  The first screen snapshot below shows that the last 2 Command ships require that The Sovereign Immunity technology  is required.  The second screen snapshot shows that I have researched the Sovereign Immunity technology.  The third screen snapshot shows that the last 2 command ships are still not available and now do not show any additional required technology.

Here is a link to a save that will show that the Command ships are not available:

https://www.dropbox.com/scl/fi/j7pp95mc7u463r65jt7qd/Command-Ship-Availability-Issue.GC4Sav?rlkey=1hs3pmtretc1v3xveewq38uu6&st=b76x22ts&dl=0