To overcome the limitation with the <MultiGeometry> element, I am considering splitting my data into several rows as hinted at in the Fusion Table Help and here.
This will yield a large amount of rows and I would like to group them into Folders in Google Earth when viewing the Network Link. Is that possible at all ?
Note: there is a similar question left unanswered on the Fusion Table forum.
At the time of writing, this is not possible.
There is already a related feature request asking for Folder capability (as well as Sub-Folder incidentally). Wait and see, hopefully Google will address this in the near future.