Example 1: you use two versions of mame, play some games in both versions, with some of those games have different zips and others have the same. You could have two rom folders: mamexyz/roms has all the roms, mameabc/roms has just the changed roms, and mameabc/mame.ini has both folders in the rompath.
Example 2: you have small harddrives (or thumbdrives or CDs or DVDs) and can't or don't want to put all your roms on the same drive. Heck, you can share folders over your local lan between computers (see next).
Example 3: you have two cabs, say horizontal and vertical, each with the respecitive ROMs. Rarely, say cab Vert is in use and you have to play a vert game so you dicide to play it on the horizontal cab, but the ROM is over on the vart game only. If the ROM folders are shared between the two cabs, you can without crowding either cab's "primary" ROM folder with the "wrong" games.
Example 4: you're sharing ROM over P2P weird and like to separate, say, the neogeo roms from all the other roms, or the non "u" release ROMs for the new "u" roms.
It's commonly needed, but a great feature, IMO.