Also include mainline beta flags in storage file

Previously, both prod and exported mode codegen would use device_config,
therefore, no need to store the flags in new storage. Now exported mode
codegen would rely on new storage due to its safety. We need to keep the
flag values stored in both legacy and new storage.

Bug: b/406508083
Test: atest -c
Change-Id: I07d70deaff493cf30e991fb51ff84dd3871a3adc