I ran SDTM checks on my datasets where i have custom datasets. Since the custom dataset names would not be in the SDTM CT for DOMAIN, these DOMAIN values should pop-up as issue, but I could not find these.
For your CT checks, are you doing any different for extensible CT? I am assuming it is reporting any code values which do not match to SDTM CT irrespective of the extensibility of the CT. Is this true?