Lemme clarify why:
I try to store as much program data on drives different then C:
Thay way I can keep the configuration for the program, even when I reformat.
Most of the times, when the program stores it's files in a subdirectory, I create an NTFS-junction to my configuration storage
directory on another drive. That way, I only have to backup that one folder to backup all settings of programs that save them
to disk and I don't lose them when I reinstall my PC.
Plus it would be handy to have all files that matter nicely together in a directory, even for normal backup-purposes.

Thanks.

To be compliant to Windows rules, we have to keep configs in User Profile directory and probably it's what we'll do for the next major version.

Excellent, as long as it's collected in one folder it doesn't matter where it is located