Ahh, OK, I see! I never used any of that, nor did anything like you mentioned, when I’ve tested hackintosh, so I never had to have this concern about onboard graphics enabled or not.
So your concern here is about functionality of the OS for what you want to do, needs onboard graphics enabled too, not the install of hackintosh in general.
Most/all desktops disable onboard once you connect PCIE card. Laptops, 95% have onboard enabled always, otherwise no display out. In rare/expensive laptops, sometimes you can switch or use both etc, but that’s not common.
Make the onboard graphics change in RU with PCIE card removed and ONLY booting with onboard graphics, I bet it stays then. Default is enabled anyway, so it should be 01 always, this is what you want 
However, as mentioned, it may not be possible, and is abnormal to have it enabled + use a PCIE graphics card, this usually only possible in certain systems or certain AMD/Crossfire situations.
Did you did notice FPRR AND BIOS Lock is in PCHSetup, not Setup or SaSetup correct? PCHSetup >> VarStoreId: 0x17 [4570B7F1-ADE8-4943-8DC3-406472842384] << This is where you change BIOS Lock and FPRR while using RU, due to this, you cannot change with setup_var, since they are not in setup.
Sorry, I forgot to mention above!
Here, dump vars for me, I will edit to disable BIOS lock and FPRR (these both, or at least one, may still be enabled in “custom” NVRAM too, outside of their normal varstores)
Download the following package, and run the command below from each versions folder that directly contains it’s exe.
Once done, copy the entire folder somewhere, delete everything but any created vars.txt and then repackage this and send to me, this way all created vars.txt remain in place in the folders of the version that created them.
http://s000.tinyupload.com/index.php?fil…212104496994806
H2OUVE.exe -gv vars.txt
I’ll check the BIOS about menu mod for you now too, thanks for the dump 
* Edit, we may be able to force enabled only, by editing setup and replace the disabled option, so the min/max is 01 only
Or similarly, make both options enabled only, so no matter what it switches to it would then = enabled.
like so >>
Onboard Graphics Controller, VarStoreInfo (VarOffset/VarName): 0x12D, VarStore: 0x16, QuestionId: 0xCE0, Size: 1, Min: 0x0, Max 0x1, Step: 0x0 {05 91 72 1C 73 1C E0 0C 16 00 2D 01 10 10 00 01 00}
One Of Option: Enabled, Value (8 bit): 0x0 {09 07 03 00 00 00 00}
One Of Option: Enabled, Value (8 bit): 0x1 (default) {09 07 03 00 10 00 01}
Or this may also work
Onboard Graphics Controller, VarStoreInfo (VarOffset/VarName): 0x12D, VarStore: 0x16, QuestionId: 0xCE0, Size: 1, Min: 0x1, Max 0x1, Step: 0x0 {05 91 72 1C 73 1C E0 0C 16 00 2D 01 10 10 01 01 00}
One Of Option: Enabled, Value (8 bit): 0x1 {09 07 03 00 00 00 01}
One Of Option: Enabled, Value (8 bit): 0x1 (default) {09 07 03 00 10 00 01}
* Edit 2 -
After looking at your AMITSE, you do not need AMITSE edit here, probably only AMITSE/SetupData edit to change Access Level to User or Super at ROOT of setup, which you can do with AMIBCP
Should arrive next week. 
