Why INTRUDER# measures 3.0V or lower on the multimeter?
INTRUDER# has a very weak pull-up (1MΩ). If you touch the probes, skin resistance is enough to pull down the voltage a lot (like less than 1.5V). Even without touching the probes, the internal impedance of the DMM (typically around 10MΩ) will cause it to drop to around 10MΩ*3.3V/(10MΩ+1MΩ) = 3.0V.
Can I use a different SPI ROM part number?
Better use the original part number.
If you can't get it and you have an Intel platform, use UEFITool to check what part numbers are registered in the VSCC table and use one of these.
If you have an AMD platform, I'm not aware of something similar to the VSCC table, but compatibility could still be an issue. Be sure to check operating voltage, size, maximum frequency and dual/quad SPI mode.
I am missing VCCAXG/VCCGFX/VCCGT (iGPU core voltage), how do I solve it?
The iGPU core voltage is almost never relevant. It typically only comes up when there's a significant load on the iGPU. It can often be seen spiking a couple of times on the oscilloscope when POSTing.
In other words, it's generally normal that it's missing. If you have some kind of issue with the machine, the cause is most likely elsewhere.