if you're u sing the latest BETA build then the closed captions should be in sync with the commerical cutting. There are 2 parameters used to adjust the timings of the closed captions (one static offset and one incremental offset which you're
referring to). See the documentation for more details on the 2 parameters in mcebuddy.conf
Regarding your request, use PreConversionCommercialRemoval=true in your profile to remove commercials prior to extracting CC's