Whether CAS items or objects, the point is to un-check "Renumber/rename internally" when cloning in s3oc.
You can not use TSRWS for making default replacement files.
I'd like to explain the process using a plant as an example.
1) Open s3oc and select Cloning > Normal Objects. Then s3oc starts reading object catalogue. Wait for a while.
3) Un-check "Renumber / rename internally", and click 'Start' button. Save the package file somewhere you like.
4) Open this package file in s3pe.
In the case of my default override of EA's flowers, I edited their FTPT and OBJD. So I deleted other resources than FTPT and OBJD.
5) In resulting file, edit the resources with s3pe as you like.
The steps 4) and 5) will vary depending on which resources you want to edit. In any cases, edit the resources which you want to override, and delete other unnecessary (same as default) resources.