Hello and thanks for this very useful direct update guidance!
I ran myself into the issue of not being able to boot from
Boot macOS Install as it was not available at Clover screen. But at some point I wanted to do clean installation and I booted from
macOS Sierra USB (after running macOS Sierra installation in El Capitan and reboot). I was able to finish update and works flawlessly. To summarize I suggest an intermediate point between 4 and 5 to the above guide:
4,5. Boot from macOS Sierra USB (and continue with installation as indicated in steps 5 thru 7).
I didn't have any issue due to Boot Options not being set as indicated in the guide.
My system:
MSI Z97 Gaming 5, I7-4790K, 16GB DDR3, nVidia Quadro M4000, Samsung SM951 512GB -AHCI- MZHPV512HDGL M.2 2280 PCIe PCI-Express 3.0 SSD