ImageMagick has some optimizations to reduce the file size when the PNG file is saved to disk. You can prevent this by forcing the format to PNG32. Below is an example of how you could do that:
montage "%ImgPath%\layer_0.png" "%ImgPath%\layer_1.png" -alpha set -geometry 1500x1500+25+25 "png32:%ImgPath%\lkjdsafd.png"