The bundle environment has three parameters for spacing.
\GapDepth
means minimum height of gaps between
adjacent nodes.
\GapWidth
means minimum width of gaps between
adjacent nodes.
\EdgeLabelSep
means height of an edge label
from the lower node of the edge.
You should set these parameters before the bundle environment if you dislike default values.
If you write
\begin{bundle}{xxx} \chunk{aaa} \chunk{ \setlength{\GapDepth}{5pt} \setlength{\GapWidth}{5pt} \begin{bundle}{yyy} \chunk{bbb} \chunk{ddd} \end{bundle}} \chunk{ccc} \end{bundle}you get