Generating custom catalogs from a small set of visit images and their templates

Yes, although you need to start using butler. There are other people investigating using their own data in the Rubin pipelines. See for example the discussion here:

It’s a bit tricky to set up a butler where you haven’t started with raw exposures and want to go straight to processed visits, but it is possible, albeit we don’t really have any tooling for that to calculate the detector regions for you from the FITS WCS, for example.

If you look at the software paper (PSTN-019) you will see a discussion of a lot of the issues, including fake source injection.