For me, it was an aesthetic thing ... access to the terminals is on the bottom of the tower portion, which works out to be the Woofer end.
So rather than have the Woofers and the wire bundle in the center area where it could get snagged as people walk through,
I simply stacked them the other way to be neater and expedient when I set them up.
Maybe I'll restack them the other way next time I have some time ... but frankly they sound pretty good as they are now ...