Options will be included. The only time option packages affect the residual value is when a manufacturer has separate residual values for certain trim levels. For example, the Audi A4 S-line models have 2% lower residual value compared to models without the S-line option. Also, the Avant body style has 1 or 2% lower residual compared to the sedan body style.
I am also looking at leasing a 2007 X3 (24 mo/12K per year) in about 9 months when my 2006 A4 lease is up. The residual value on the X3 is incredibly high.