When applying SecUpdate2018-004 to previous SecUpdate2018-003 installation on El Capitan, HEADS UP. There were TWO SecUpdate2018-003 updates for El Cap, an initial and a slip stream version that Apple very quietly slipped in to replace the initial one a few days later. If you installed the initial SecUpdate2018-003 download, the build number shows 15G21012, if you waited and downloaded it after Apple replaced it with the new one, the build is 15G21013 when completed..
NOW, if you try manually try to run SecUpdate2018-004 over SecUpdate2018-003 build 15G21012, it will refuse and say the SecUpdate2018-004 update can not be installed. Run it over SecUpdate2018-003 build 15G21013 and no issues. I had to first RE-APPLY SecUpdate2018-003 (the newer one and the one you get currently if you download a fresh copy from Apple) to get the build number from 15G21012 to 15G21013. Then I was able to apply SecUpdate2018-004 (which results in build number 15G22010 btw).
I don't know if it would have worked had I gone through MAS ; I always apply my updates by manually running the installer BECAUSE I always boot from another drive to run update. That's a tip everyone should follow, i.e. never boot from and install an update to/from the same boot partition. In my experience, this virtually eliminates the reports you hear about the update taking forever, and or the system taking forever to reboot, or runs slow after the update. This is because by booting from a different drive, the one you are updating is completely accessible and files can be updated quickly without delay. If you try to update the same drive you boot from, not all files can be updated first time around because the system is still running, its like trying to replace a rug while you are still walking on it. it takes a few reboots and a lot more time before everything is updated. With disk drives so inexpensive and HUGE these days, there is no excuse not to have an external boot drive or to divide your existing internal drive into multiple partitions, plus macOS is SO easy to clone and excellent cloning software is readily available (Chronosync, SuperDuper, CarbonCopyCloner to name just a few). In any case, for emergencies, you should ALWAYS have another boot option available to regain access to your working partition in case of trouble.