USDC files are designed to allow appending new information to the end of the file without having to re-write the entire file (which might be many gigabytes in size). So you can “delete” data from the SdfLayer (and/or add a few new attributes or prims), save the modified file, and only a few kilobytes of new data get appended to the end of the file. The many GB of preceding data is not re-written. Huge performance win. At the cost of some “dead” disk space.
The save-to-another-file-then-move is the right way to do this when you have decided that the time cost of writing the complete file is worth it for the amount of disk space you’ll be saving. I’m not sure if there is a built-in SdfLayer API for this, but I think it would be nice if there was. Seems like it would be a common thing for one to want to do.