Is this a limitation or is there a way to get the RAW to collect the actual shutter time?
You mean Canon raw I guess? It's not unusual for the canon EXIF or display not to properly record the overrides. For jpeg at least, the canon "maker note" section of the EXIF is more frequently right, don't know if there is anything similar in Canon raw. It may be possible to set an additional propcase to get the override value recorded.
CHDK DNG should record the override time, but this probably doesn't justify using it on cameras with native raw.