A binary blob as a configuration store is unambiguously wrong.
The difference between all the bins and all the sbins is clearly explained in the Linux Filesystem Hierarchy Standard. It's not Linux's (or UNIX's) fault if someone doesn't read or follow that.
This isn't really an argument for the windows registry (it's a whole separate filesystem just for configs? With none of the versioning, inheritance, whatever features you want for configs?), but it is another way to think of it.
There might be an argument to be made but it's clearly not unambiguously wrong.
In practice, almost everything is binary, string or DWORD.
The world would have been a very different place if the registy had supported comment fields and/or online help.
But you have to weigh that advantage over other advantages. If it was this simple, every database (and we are talking about a database here) would just be text to make recovery easier.
Explaining a confusing standard does not make the standard clear or good.
It's a very poor designer that blames their users.
Would you call someone out writing a Windows application that didn't install its binaries under PROGRA~1? Same principle.