System Keychain Certs Import fail with UNIX[Operation not permitted]
The issue is that, somehow (not sure how), the extra restricted flag was add to System.keychain which meant it could not be modified while the system is running. Thus, it was SIP protected. I followed this guide to correct the issue. 

(From the guide) You can check if your keychain is restricted using the following ls flags in the Terminal

cd /Library/Keychain
ls -@Oaen


My original output had the following info --- note the restricted flag on System.keychain.

total 536
drwxr-xr-x  11 0  0  -             352 Jun 21 08:54 .
drwxr-xr-x+ 66 0  0  sunlnk       2112 Jun  4 17:28 ..
 0: ABCDEFAB-CDEF-ABCD-EFAB-CDEF0000000C deny delete
-r--r--r--@  1 0  0  -               0 Jun 15  2016 .fl043D1EDD
    com.apple.quarantine        29 
-r--r--r--   1 0  0  -               0 Jun 15  2016 .fl947E1BDB
-r--r--r--   1 0  0  -               0 Jun 21 07:59 .flD2C1AB74
drwxr-xr-x   2 0  0  -              64 Jun  4 17:32 SupplementalsAssets
-rw-r--r--@  1 0  0  restricted 124792 Jun 19  2016 System.keychain
    com.apple.metadata:_kTimeMachineNewestSnapshot      50 
    com.apple.metadata:_kTimeMachineOldestSnapshot      50 
-rw-r--r--   1 0  0  -           33208 Jul  1  2016 System.keychain-orig
-rw-r--r--@  1 0  0  -           53488 Jul  1  2016 apsd.keychain
    com.apple.quarantine        29 
drwxr-xr-x   3 0  0  -              96 Jun 21 07:50 crls
-rw-r--r--   1 0  0  -           53248 Jun  4 17:32 pinningrules.sqlite3


To correct this, you have to boot into recovery mode. Hold down CMD-R during reboot when hear the chime. When there:


Open DiskUtility and check to make sure your main disk is mounted. It will not be if use FileVault to encrypt it. If not, mount it by entering your password. Quit DiskUtility.
Under Utilities menu, you can open a Terminal, change directory to keychain folder and edit the restrictions. (Note your volume name may be different if you have a non-standard installation.)

cd "/Volumes/Macintosh HD/Library/Keychains/"
chflags norestricted *

Check the ls -@Oaen and you should not see the restricted tag.
Exit Terminal and reboot.