Hi,
The transparent box is

something which I have added to show the boundaries. I didn't check the original GPX file but as the waypoints are spread out too far apart, the bounding box's roof is partly falling below the earths surface, I guess. It is only visually interesting on smaller surfaces where the earths curve is closer too a straight line. I should but some code in to compare minlat-maxlat and minlon-maxlon to set some limit on transforming these attributes to the box.

Yes, it is just another placemark so you can de-select it.
I could also de-select it by default.
I will probably create some input form in my GUI application sothat one can customise the XSLT -transformation process( with some PARAM values)
Open, visibility and whether the track needs to have points besides a path.
Well, you can easily delete the boundary placemark aswell as the empty routes and then save the KML/KMZ file to and open from local host.
Don't understand why GE start boven the ocean I'll check the file tonight in GE.
Cy