The Windows ssh client pulls its config and keys from %USERPROFILE%/.ssh/, as does the Git for Windows ssh-- they can and will share the same config as long as

The Windows ssh client pulls its config and keys from %USERPROFILE%/.ssh/, as does the Git for Windows ssh-- they can and will share the same config as long as the config's valid for both (OpenSSH is the same release, but the Windows build uses LibreSSL instead of OpenSSL, so you could conceivably write a config file that isn't compatible with both, I think?).