The Apple TV remote is rechargeable. I've charged it once since buying it over a year ago. A rechargeable tag could last as long as or even outlast a coin cell. It's just sending out pings which is why it lasts so long. You're somehow associating a rechargeable battery to what you have to do with your phone or watch that you have to charge every night. Rechargeables with low energy requirements can and do hold power for a very long time.
Apple likely used a coin cell to keep the cost down in the first generation of an unproven device. An economy of scale will enable the COG to come down in the next generation, which will help make it thinner and use more complex circuitries and components for the same or lower cost than the previous gen. Everything Apple has made has followed this model.
