Had similar challenges with overlapping areas in mosaics and had to cut away corners.
Cropping the corners can be done with PixelMath by simply creating a black rectangle or circle over the bad areas of the single mosaic piece.
PixelMath offers the processes:
maxd2rect for rectangles at any place in an image and
rdist for circles at any place in an image
For example:
to cut away a black rectangle at pixel position 150,210 (x,y) in the size of 100,80 (width,height) pixels
the Expression in PixelMath is:
d = maxd2rect(150,210,100,80); iif( d > r,gray, $T )
In the "Symbols:" line of Pixelmah you have to (!) enter: d, r = 1, gray=0.0
Gerald