At one time, they did number the apparatus Engine 3, Engine 6, etc. They switched to go in in line with the present system established by Westchester County, sometime in the late 70's/early 80's I think it was. I'm honestly not sure why. The only units in Yonkers that I can think of that aren't bound by the numbering system are the Chiefs. If you want to see an interesting set up, look at Continental Village up on the Westchester/Putnam Border. The rigs there are not only numbered for Westchester, but numbered for Putnam as well, 14-2-2, 14-6-1 etc.
What's so strange about the way Westchester does it?? Engine 185 from Somers, Engine 58 in Port Chester. Seems pretty cut and dry. Yonkers is a city in Westchester County, however, if they go mutual aid and operate on the Westchester frequencies, they could be confused with other units. Mount Vernon numbers their rigs Engine 1, Truck 1, but if they go over to Pelham, they are Engine 201 or Ladder 62.