According to LEED Commercial Interiors SSc3.2 - Alternative Transportation: Bicycle storage and changing rooms template, if a bicycle storage is located within the building, the distance must be considered zero. Can I consider this to LEED CS also? And does it mean that every bicycle storage located underground can be considered within a building, and, consequently, distance zero?
It depends on how far the bike storage room is from where people enter the occupied area of the building. The garage area itself isn’t considered part of the certified LEED project area, so if the bike parking storage is in such a large underground garage that people have to walk more than 200 yards of horizontal travel to reach the entrance of the LEED building or elevators that serve the LEED building, then that storage probably wouldn't count. You can check the sample Core & Shell LEEDOnline credit template to compare the wording with the Comercial Interiors SSc3.2 form you mention.
https://new.usgbc.org/sampleforms/Core%20and%20shell/all/all