This falls in category "throwing ideas around"
It might be possible with imagemagick (IM) in a batch file.
There are plenty of 'if-n-buts'
IM still does not handle xcf files very well. Better than it used to but so far I have not been able to preserve transparency when there is any, which also applies converting xcf to png with IM.
Same applies for outputing to a multilayer xcf file. However tif does work.
This is in linux but I suppose there are similar commands in Win.
#!/bin/bash
#
# list is the file with the list of files to combine, one per line
list=$1
#
# uses Imagemagick to stack the images to a new file multi.tiff
while read FILE; do convert "${FILE}" multi.tiff -type TrueColorAlpha multi.tiff ; done < "$1"
#
# opens multi.tiff in Gimp. there is a dialog to ok
gimp multi.tiff
#
# tidy up
rm multi.tiff
Very rough, throws up an error on the first iteration because multi.tiff does not yet exist, but does work.
looks like this
http://i.imgur.com/xVXt75Q.jpg