Windows-specific Git configuration settings; where are they set?

As this commit explains, they’ve added another config location only for Windows, which is applied even before the --system:

The file /etc/gitconfig can be used to store a system-wide default
configuration. On Windows, configuration can also be stored in
C:\ProgramData\Git\config; This file will be used also by
libgit2-based software.

…

On Windows, as there is no central /etc/ directory, there is yet
another config file, intended to contain settings for all
Git-related software running on the machine. Consequently, this config
file takes an even lower precedence than the $(prefix)/etc/gitconfig
file.

So I believe you can find those mystery settings in C:\ProgramData\Git\config.

From that commit I can see that git config --system --list should’ve shown you those settings, but it seems that the absence of C:\Program Files\Git\mingw64/etc/gitconfig file aborted the operation, which is probably a bug.