Only add packageOps if they don't already exist in systemReady

We were overwriting them when we try to initialize for all remaining
packages that didn't have state from the persistence read. Also we need
to be sure to add Op objects for codes that weren't added during the
earlier recent_accesses round.

Test: Boot and dumpsys
      Verify new testcase with and without fix
      Verify persisted files in upgrade cases and normal boot cases
Fixes: 273813938
Bug: 272810483
Change-Id: Ibf814b9a3318420d49a77c35f0bab7e6763f8953