KMZ is a compressed archive, so text editors and many scripts cannot read it directly. TopoJSON is much smaller than GeoJSON for adjacent regions. KMZ is at home in KML with its icons and overlay images in one file; TopoJSON is the usual choice for compact boundary maps for the web.
Every format is read into plain GeoJSON features and written out from there, so coordinates, names and properties carry over wherever the target has a place for them. XML that declares custom entities is refused, and KMZ files are parsed without touching the network. The KML inside the KMZ is read; icons and overlay images in the archive are not carried over. Coordinates are kept exactly (no quantisation) and shared borders are stored once; features without a shape are left out.