A possible work-around might be to set the hole bit on the cell headers that you apply the skew transform to.
With the hole bit set, the scale handles won't try to use the skewed cell rotation for the handle points and will instead compute handles oriented to the selected component. So to be able to scale this cell along the red line you could select the cell on the line component that's connected to the filled circle/parallel to the red line.
Tapping alt with the handles displayed toggles between the component oriented handle set and view aligned handle set. I still need to look into why the normal cell handles are so off, but that's not likely to help you in the current version.
HTH
-B
