Yes, of course. The customizer will continue to have the ability to include or remove the media queries for these. You can also always make a local build on your own to do it.
Just that the client didn't want the two different sizes for desktop. Nothing in particular, just didn't have time to invest into that and it wasn't really providing that much benefit for the site we were working on.
Will we still be able to easily remove things like the "large desktop" size?