I am also having similar issues. Some layers are correctly placed, but layers that use clipping groups or blur effects are not placed correctly. I am not really familiar with illustrator scripting, but I looked at the script, and to me it looks like the script is checking the position, height, and width of the vector layer in the "parselayer" function and using that to determine the position. THis creates a problem because If you use certain illustrator features such as clip groups The rasterized artwork may not have the same size as the vector art and therefore the positions may get messed up.
I suspected this might be the problem, so I tried to correct the positioning by creating a bounding box in the form of an empty (invisible) rectangle in problematic layers that was big enough to cover any data that is unseen in the blend effect or clip group. This gives me correct positions, but it is wasteful because the images now have a lot of wasted space.
I believe that modifying the script to include a rasterization step in the parselayer function to rasterize each layer before parsing the position would fix the position issue, but I am not sure.
Also, positioning in spine is also incorrect if the user choses anything other than 100% scale (the 100% scale positions are used, the positions should also be scaled)