The TP serializer is "smart". It doesn't serialize the entire document every time. Instead, it tries to do a minimal update. For these settings, it does so in TargetDefinition.updateIUContainerElements(). This code compares the old nodes with the new ones, and if any changes were made to the repository or the Installable Units, this is reflected. However, it doesn't look at the location itself.

See the self-explanatory video below. If you're wondering, saving the file does not solve the issue.