Large-value ceramic caps  in small packages?
It is very likely that the 1206 ceramic cap and the large stacked ceramic cap differ greatly in one very important characteristic.

ESR

The larger cap can probably handle much larger surge and RMS currents, and likely has significantly lower ESR.

Remember, there is more to a cap than voltage and number of uF. If you're putting the cap in a big DC-DC that dumps 10A into the cap every switching cycle, and the 1206 cap has an ESR of .05 Ω, it'll get really hot and fail in a hurry.

The big stacked ceramics are typically used in extreme-duty power supplies, where a tantalum or electrolytic cannot handle the conditions.