Apple may well use a firmware setup that is different to the norm.. Apple drives always have apple logo on them.
Spin down even with Apple drive may not work on gen2.. I tested it and found issues..
ie I removed a 3TB drive from a Gen4 and installed it in a Gen2. The drive had spin down issues.
I installed an off the shelf 3TB drive in the Gen4 and it had no issues spinning down.
Spin down issues vary with brand of drive and other more esoteric issues.
http://www.ifixit.com/Device/Apple_Time_Capsule
We used to find hitachi drives spin down ok.. WD did not.
But firmware on drives is constantly being updated. Take your best shot when you want to be a modder of products.. expect life to get hard.
It should work with 4TB drive.. they have even higher current demands.. the Gen2 power supply will not work.. or work for long.