One issue with his 48 fps shooting style for The Hobbit Trilogy was that in order to make the conversion to 24 fps easier, he had to use a shutter speed other than the rule of 180. It made the motion kind of weird looking. 48 fps with a 180 degree shutter angle actually can look pretty good...
He considers the extended cuts to be the best cuts if you don't have time limitations. In TT and especially ROTK, there are whole story sections cut from the theatrical version for run time that only make sense once you see the extended cuts.
There is no "director's cut" per se. Peter Jackson considers the extended cuts to be his best version so far without the time limitations associated with a theatrical release, but still likes the theatrical cuts as well. He would still like to do a super cut one day, but has yet to do so.
Actually, you are not purchasing anything in a digital form. Read the usage agreement. That's like building a collection on sand. The iTunes version still has lossy audio and lower bitrate video. Dolby Atmos in lossy form is even less sophisticated than the lossless TrueHD version.