Basically there are two main dimensions to a character described using KanjiVG:
1) The layout, which is the path information that forms the kanji.
There should be as many paths as there are strokes ; ideally to keep
things coherent a path should be a slightly rearranged copy of another
path of similar type (the number of control points *might* become of
importance for some applications, so paths of the same type should
have the same number of control points).
2) The semantics of the character, e.g. its components, sub-components
and how they relate to each-other.
There are quite a few good tools for 1) (e.g. inkscape), but very
little for 2), which is basically done by copy-pasting as far as I am
concerned. All the same this data is hard to visualize. So a web tool
that would address these issues would be most welcome.
Note that I come to believe less and less that such a tool should be a
direct reflection of the information represented in the .svg. SVG is a
purely hierarchical format, and that constraint does not really
reflect the reality of how kanji information is organized. For
instance, as you noticed some components are split in two, and these
two parts might not even share the same parent. A tool that provides
an easy view and editing capabilities of this kind of fact, and that
is also capable of outputting the corresponding svg, would be a great,
great help.
Actually, and if that's what it takes, I am not at all against using
an alternate source format that would be better suited for this kind
of work, with SVGs being generated from it.
In any case this will require some thorough thinking, but if you are
willing to take on that task, this would be a great contribution to
this project.