OK, guys. I solved all the problems, and am now on Sierra 10.12.3.
1. First, before trying to update from within El Capitan, I wished to have a good Sierra USB Install Disk, in the sense that it should have been working for my old bios system, and old Nvidia graphics card. So, always using Tonymacx86 Sierra Install USB (UniBeast + MultiBeast), I made many frustrating tentatives, but I couldn't never reach OS X installer: the boot gave a kernel panic after having loaded NVDAStartup.kext. I looked around, and I found that a possible solution was to set, in the config.plist of EFI/CLOVER folder of boot usb disk, of course using Clover Configurator (google for finding), the modifiers Inject Nvidia, NvidiaGeneric and NvidiaSingle in the Graphics section. Note that to do so, you must mount EFI partition by terminal, or by Efi Mounter v3 (free for downloading). Alternatively, Clover Configurator asks you if you wish to mount EFI partition, if you did not.
Once that this was done, at Clover boot I needed to set modifier nv_disable=1. This is mandatory for older nvidia graphics card, but could be necessary for newer as well.
2. I was then able to reach the OS X installer, and installed Sierra 10.12.1 on a test drive. Note that either the installer and the newly installed system work at a low screen resolution, but this will be fixed later.
3. I booted the new Sierra OS X, as necessary, starting a last time using the USB Install disk, and installed boot loader on the Sierra drive.
As I knew from previous investigations, I had copied the old El Capitan NVDAStartup.kext on the install disk, as well as others kexts I needed, on S/L/E (AppleHDADisabler and VoodoHDA), and installed all the old kext by means of KextBeast. Then I open the config.plist (Sierra HD EFI/CLOVER partition) and left only Inject Nvidia checked.
4. At reboot I had my new Sierra 10.12.1 perfectly working on the test drive. Not really perfectly, I experienced for the very first time the well known shutdown issue (on real Macs as well). I will explain later, in another post, the possible solution I found to this very particular problem, annoying new mobo systems as well, and in my case also very dangerous, causing a loss in the mobo bios, which fortunately has an automatic recovery.
5. I then updated my old El Capitan installed on a EVO SSD, to Sierra 10.12.3 (the last downloaded version), following a similar procedure. In the sense that I changed my EFI/CLOVER config.plist setting all the modifiers above, before upgrading. Then, at System reboot, I set, as before, nv_disable=1 modifier at the clover boot, and reached (in low resolution) the Sierra Install procedure. At the end, I entered the same modifier, and reached the new Sierra 10.12.3 desktop in low resolution.
Then I reinstalled the older kexts, re-edit config.plist leaving set only Inject Nvidia. At reboot I did not set any modifier and reached a fully working Sierra 10.12.3 (still with the shutdown problem, not yet solved).
