Camera's autoexposure happens before overrides. So if you have a fully automatic mode from your camera enabled AND you have CHDK Tv override, you will get Canon's ISO and Av/ND filter selection, and the overrided Tv will be used. Usually the exposure is not correct unless you by sheer luck happened to override to whatever Canon autoexposure had selected.
So yes, you must set exposure compensation to fix exposure if you want to or have to use autoexposure.
Canon's MakerNotes section of the JPEG EXIF tag actually has the correct overrided exposure settings recorded, btw. Most apps just don't know how to display those (no, CHDK doesn't write them there, the camera does... even without CHDK those values are more accurate than ones found in standard EXIF tags, but they don't look familiar because they are the camera's approximation of real APEX values instead of rounded/convenient/familiar "market" values displayed on Canon's OSD).
