FWIW, I did a direct upgrade from 10.11.4 to 10.12.3 using, basically, the instructions in the OP. I followed some steps that I found necessary in the past, however, and you may or may not need to do any/all of them for success (and some may have created problems for me initially, not sure...).
1. Make bootable backup of entire root drive using CCC.
2. Mount EFI partition on SSD of my Fusion drive
3. Backup Clover directory from EFI partition
4. Download and upgrade Clover. Look afterward to see if clover upgrade actually applied to mounted EFI partition rather than simply putting the install in /EFI (this happened to me before when moving up to El Capitan, no idea why).
5. Copied all the kexts (including fakesmc.kext) I had in EFI/CLOVER/Kexts/10.11 to EFI/CLOVER/Kexts/Other (at some point, I don't remember when exactly, I *also* copied these kexts into the 10.12 directory).
5. Download Sierra installer from app store
6. Run the installer and point it at the correct drive. Reboot.
Now, upon reboot, "Boot MAC OS X" was *not* an option displayed in the Clover bootloader menu. So, I tried booting back into ElCap (still an option there), but no dice. It would not boot. So, I tried again, this time with -v, nv_disable and NoCaches=1. Verbose mode showed me an error I'd seen in the past related to SIP. So, I rebooted into my backup ElCap, and changed config.plist on the SSD EFI partition to disable SIP.
I booted again, and though "Boot MAC OS X" was *still* not an option, booting with the entry for ElCap actually booted the installer. The rest of the install went fine. Each time a reboot was needed, I used -v and nv_disable. When I finally got to the desktop, I got prompted by the Nivida driver app to download and install new video drivers for my GTX 960. On reboot, I left the default flags in Clover, and got straight to the desktop without issue.
Only other issue encountered was sound was again broken (no audio devices). So, I went and got the updated version of Toleda's Clover ALC script here (
https://github.com/toleda/audio_CloverALC/blob/master/audio_cloverALC-120.sh), and ran it from a terminal. I rebooted, and sound was fixed.
iMessage and all iCloud related services continue to work (as expected).
Only annoyance is that I now need new drivers for a few things like a printer, and just discovered a bad bug in Logmein under Sierra. But everything works great.... good luck all!