Columns in Type II-F.R. buildings are required to have a 2HR fire rating based on Table 6-A (columns are part of the structural frame- refer to Section 601.4).
By the way, Section 602.5 "Roofs" that you mentioned in your post refers to Type I-F.R. buildings (not type II-F.R; that would be Section 603).
The fire-resistive protection for the individual columns should cover the entire length of the colums and not stop at the 25 ft mark.
My concern is when reading CBC 602.5 Roofs Par. II "When every part of the structural framework of the roof of a Group A or E Occupancy or of an atrium is not less than 25 feet above any floor, balcony or gallery, fire protection of all members of the roof construction, including those of the structural frame, may be omitted". According to "601.4 Structural Frame" includes columns. Do you or anyone else believe CBC 602.5 is including columns to be unprotected where the roof structure is above 25 feet?
Just out of interest, the 2007 CBC assigns 1HR rating for structural frame (Table 601) of Type II-A construction instead of 2HR in the 2001 CBC for II-F.R. construction.
There is no equivalent section in the 2007 CBC similar to Section 602.5 of the 2001 CBC.
In the 2007 CBC, the individual protection of structural members is in Section 714.2.1 and 714.2.2 (specifically for columns).