Is this possible or is the only way to make and apply the cropping to virtual copies?
Yes, if you make an additional complete set of virtual copies. That way the cropping differences will be ignored by the other collections the images may also be part of.
I do this all the time for printing various aspect ratios ... I may have the same image in a collection for 4x6, 5x7 and 8x10, etc. ... but each collection has it's own virtual copy for that specific collection and crop aspect ratio. I also add a color label and keyword combo to quickly identify the different virtual copies when I may view them outside of the collection.