I have had a similar problem with matching up parts of incomplete but overlaping maps.
See discussion.
viewtopic.php?f=1&t=22526&p=95286&hilit=overlap#p95286
The program and technique actually does not care if the search image is overlapping or not, but it did have to deal with the transparency problem.
To avoid the 'transparency' issue, I grabbed sub-sections of the search image that had no transparency (using dilate to mask sub-image selection). Also to prevent selection of a sub-image that contained no useful search pattern, I also selected the sub-images by centering them on areas of high-entropy (lots of color changes).
The selection is skewed to actually look for the sub-images around the edges before trying one in the middle, (next sub-image is the next valid center point that is furthest from all other sub-image attempts so far) but that is because the focus was on 'overlaps' but it really did not care if the result was an overlap or fully contained.
NOTE original and real reason for using small sub-images for the search was not transparency (though it solved that issue), but for speed in searching the larger image for possible locations of the new 'overlapping' image, the exact same technique (and program) should work for you in finding the location of the 'transparent' shaped image on the larger image.
The script
http://www.imagemagick.org/Usage/scripts/overlap
currently is set up to continually find matches until 3 sub-images match the same location, and to abort (no match) if we get 3 different matches! Otherwise it aborts if the distance between sub-images is getting too small (that can take a long time).
Basically it means it needs to find 3 sub-images of the search images that matches to same 'overlay' location. While a 'match' is simply a threshold of the default output of "compare".
These are hard corded in the script for my purposes, but the script is very well commented and you can adjust as you like, or generate your own, now that the technique has been worked out.