You can switch to using the Use Default Group Directories for the default virtual directory mapping mode and then create a group with the %USER% variable in the virtual directory path to mimic the previous default option.
For example, let's assume your Global Home was set to C:\ftproot.
You would create a new Cerberus group and add a virtual directory called home to the group's directory list (you can actually name it anything). Make the path for that directory C:\ftproot\%USER%. You can then control the permissions on that directory like you would for any group's virtual directory.
When the user logs in the username will be substituted for the %USER% part of the path or name. If you enable "Is Simple Directory" mode for this group and switch the default AD virtual directory mapping mode to this group then you've just duplicated the "Global Home\%USER%" default AD mapping mode. You also now get control over high-level permissions on the group (still subject to AD user ACLs).