Answer
This is expected, deliberate behavior: 'Install Delivery' mode updates installer_delivery.xml and <instance>_configuration_delivery.xml, while 'Install Delivery and Reconfigure' mode is what updates the base installer.xml and <instance>_configuration.xml instead. The Installer keeps these separate specifically so that installing a delivery alone doesn't silently alter your base configuration file — a delivery might carry its own default import values that aren't reflected in your actual saved configuration, and this separation prevents that from bleeding into your base config unintentionally. Note that certain delivery types (like Update deliveries or Middleware Server patches) force the Installer into 'Install Delivery and Reconfigure' mode automatically regardless of which option you originally selected. If the actual goal is just tracking which deliveries have been installed (rather than which config file got touched), check the MODULE_TAB table in the database or the 'Installed Components' window in the application instead of either XML file.