If the source code is actually GPLv3 then they should be distributing the sources without any additional charges (section 6(d) is very clear on this point). Of course, if they are the sole copyright holder they can make up additional rules, but I bristle with describing this as free software under the GPLv3. As it stands, they are implicitly dual-licensing it under a proprietary and GPLv3 license.
Personally, if I was one of the people that bought the source code, I would just upload it on GitHub since you have the right to do so.
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.
> I would just upload it on GitHub since you have the right to do so.
Hopefully, someone will do this. It makes me wonder why they bother to charge for the download when this is an option. I guess they think they can distribute it in a more 'friendly' and 'official' manner than a GitHub link, and that some people will pay a premium for that.
Personally, if I was one of the people that bought the source code, I would just upload it on GitHub since you have the right to do so.