Making all the cells point the same way while maintaining a series connection would require jumper wires, as your diagram indicates. For low current applications, jumper wires would be ok, but adds complexity and additional points of failure. Alternating the cell orientation allows the contact plates to perform double duty, simplifies manufacturing and lowers costs. They are already doing it the “simple” way.
The reason it is prevalent in most toys and other lower end devices is that it negates the need and cost for a boost circuit. They just need to run motors, make noise and/or flash some LEDs and it is the most direct and cheapest way to design and manufacture the power system.