On TargetPanel, there is a message TargetPanel.warn ("The directory already exists! Are you sure you want to install here and possibly overwrite existing files?") shown uncondtionally.
This might be inconvenient if you want to provide an update installer, which counts with existing files in the target directory.
An option would be needed for being able to deactivate this warning and continue wit the installation.
There is already a optional ShowCreateDirectoryMessage boolean IzPack variable used for controlling a similar warning whether the target directory should be created if it doesn't exist. This approach might be enough for now.