The license determines the conditions under which you are allowed to use the program. Section 6(d) thus only states that you cannot charge others for the source code, but that does not constrain their ability to charge you.
This changes, of course, if they are using any third-party GPLv3'ed code - because then they become a redistributor of that code in which case clause 6(d) applies and they must redistribute that code free of charge.
You are restating what I said in my first paragraph -- yes, if they are the sole copyright holders they are not bound by the distribution rules of the GPLv3 in the same way as everyone else -- even if the GPLv3 did attempt to restrict the original author, as sole copyright holders they would be able to ignore the provision anyway.
I still don't agree that this is in the spirit of the GPLv3. In my view, the binaries at least are under a proprietary license.
This changes, of course, if they are using any third-party GPLv3'ed code - because then they become a redistributor of that code in which case clause 6(d) applies and they must redistribute that code free of charge.