It depends and when I say it depends, it's not just a matter of having a couple edge cases, but it is very dependent upon the application and the target audience. Assuming that we are eliminating games from the equation then there is still a wide array of applications that you may be writing where a command like is unlikely or never going to be implemented. Off the top of my head, any application targeting a mobile (e.g. iOS, Android, etc.) environment is likely going to fall under this heading.

With that in mind, in the general software space, any application that is heavily dependent upon visualization (e.g. PowerPoint, Maya, etc.) is unlikely to ever see a command line replacement be implemented. In fact, in the case of graphics software such as Maya, it is arguable a good mental exercise to determine how a full and proper command line version would work and it may not be possible to do so from a user standpoint. Thus, it is clear that there are definitively common applications that can be encountered where a command like interface is unlikely to ever be seen, or desirable even if scripting of the application may be desirable.

Next, if we look at the suggesting form the standpoint of general software architecture, I can see where it would make sense to periodically ask yourself "How can I access this feature without the user interface?" In general, if there is no way to do it and it is not directly interacting with the user (e.g. gesture input) then you likely have a situation where the overall architecture needs to be improved. In order to allow for ease of testing you are going to want to be able to directly access command without going through the user interface, even though they may not be invoked though a command line. This generally means that a solid API needs to be in place and theoretically a good API should allow for access via command line or user interface. Furthermore, in the long run, you will save yourself time if you need to add a new user interface to the application.

At the end of the day, I think that what the suggestion is trying to get at makes sense (i.e. Have a good API and build your user interface off of that) but the word selection might have been a bit better to get the point across.