So it seems synchronization, in the current implementation, is for file-level changes. For line-level changes, the explorer view is the way to go.

Perhaps "saving line-level changes in synchronization checklist" is worthy of an RFE? This would allow both file- and line-level changes in the same workflow.

Indeed, the files are not saved. That's how it works.

Version:
WinSCP 6.3.2 on Windows 10 22H2
Protocol:
SFTP
Steps:

1. Synchronize (Direction: Remote)
   
2. Compare a file (external comparison tools: WinMerge)
   
3. Copy some changes from Local file to Remote file
   
4. Save Remote file
   

Expected:
Remote file saved with some changes from Local file.
Actual result:
Remote file not changed – as if nothing has happened.

Saving changes in WinMerge works when comparing files outside of the Synchronization checklist, e.g. in the explorer UI.