Indeed, of the new Change Tracking features found in SQL Server 2008 and higher, SMO only supports scripting Change Tracking, but does not generate the commands to script Change Data Capture.
We took a look at this DCR (this is not defect but actually DCR to add suport of SMO to CDC) along with several others. Unfortunately based on current customers votes count we decided not to proceed with this DCR in the next release. However, we have taken note of this internally, and when we revisit this functionality in the future, we will try and get this implemented.
which is kind of strange considering you use SMO to re-create an existing database schema in a new schema, and maybe your T-SQL business logic relies on objects created by CDC.
Nonetheless, SMOscript 0.20 now also create the ENABLE CHANGE_TRACKING if used with the -ct switch.
As usual, the latest version of SMOscript is available for download here.