As Al Varnell noted, the increased security provided by SIP overrides simple Unix permissions and ACLs. More than once, I have had to perform SIP magic to enable deletion and subsequent new user directory tree creation in order to do a data-only migration, effectively discarding ~/Library which contained the root cause of inexplicable problems ranging from inability to open a Network preferences to mysteriously sluggish performance, all account-specific problems.
After performing the magic and migration, the contents of Notes, Calendars, Contacts, and IMAP mail accounts auto-restored while On-My-Mac mail folders were restored courtesy of Time Machine.
The real lesson for users is to avoid trying to ‘clean up’ their systems because Go64 or similar programs report 32bit apps. Unless the applications occupy many gigabytes (cough, Adobe) it isn’t worth the effort. New updated versions usually overwrite or delete older version and the macOS upgrade process is unaffected by old applications. It will become obvious after upgrading to Catalina what works and what does not. A better investment of time would be creation of a second Administrative account (see note below) as an emergency tool, along with both Time Machine and CCC or SuperDuper! clone backups.
For any new OS install on a blank system, create the emergency administrative account first, update the OS and applications, and then, as needed, migrate user accounts and, possibly, system configuration. Migration Assistant is your friend and works over many kinds of connections, including WiFi.
Most of all, have patience. Upgrading an new 2018 Mini to Catalina today, I nearly had to slap someone’s hand away while the seemingly dead system was busy upgrading firmware and rebooting several times. After then migrating the user account and system settings from an old Mini, miraculously everything the user wanted was there. It just worked™.