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It's two completely different, unrelated mechanisms of changing a job configuration.
When running update-job, it will replace the config.xml with the provided one and reload it. (POSTing should be similar). Jenkins will not modify the uploaded configuration, just like it doesn't rewrite configuration files when loading them upon startup (despite since updated plugins).
Saving a job configuration will create the XML from scratch based on the job configuration in memory after all options get processed by the various job config components.
Jenkins changing an uploaded configuration to update versions would be unexpected behavior for many users. In fact, depending on Jenkins plugins, the actual contents of the file (besides plugin versions) would change, and the user not learn about it, wondering what's going on. Currently, unloadable parts of the job configuration should show up in Manage Old Data.