Comment 7 for bug 60760

I didn't have any problem disabling and enabling autohinting in debian or ubuntu since I started using it.
I just do dpkg-reconfigure fontconfig-config
When you select native hinting, it doesn't create any symlink
When you select autohinting, it creates a symlink in /etc/fonts/conf.d/ to a file which enables autohinting.

So it seems native hinting is enabled by default. Or am I wrong?