I don't think bar end shifters care where the end of the bar is. Seems that if you cut the bars you would still attach the bar end shifter to wherever the new bars ends are. With that said, where those new bar ends are might make it diffiuclt to reach and shift the bar end shifters. You may also find that you inadvedrtantly movem them while leaning the bike against things.

Out of curiosity, what is difficult about packing your drop bars? I am 6'2" and have had some pretty wide and deep drop bars in my day. Never really had a problem packing them in a properly-sized box.