It's how this features was designed to work and it is working as it was designed.
auto-enter settings are primarily intended for entering data when a new record is created. You have the option to permit auto-enter operations when you import data if you enable the option for doing so when setting up the import.
Auto-enter should not be used to enter data that is only to be entered during import and not regular data entry. To add data to imported data without using auto-enter you can use Replace Field Contents immediately after the import to enter the data.
You can also import data into a global field with an auto-enter calculation that enters the desired data into the field. With this approach, you can disable the auto-enter for manual data entry by clearing this global field. (Learned that trick from LaRetta.)