I would not worry about the spindle threads. The spindle is forged, and the bolt will fail before the spindle does.
In all my tests, the bolts failed and the female threads did not (which is what one expects in a bolted joint of reasonably similar materials).
In all the bolts that I broke in testing, I was able to unscrew the broken portion from the female threads without a problem, indicating that the female threads were not damaged.
In the bolts that stripped (due to inadequate engagement), the bolt's threads were damaged, but the female threads were not.
I share the concern about engagement and torque values when you start mixing and matching non OEM components.
So as far as engagement, the OEM Red and Green bolts are 32mm long (the shank portion). They have plenty of engagement (if used without the protectors), more than a diameter's worth. Here is the Red bolt protruding through the LBJ, close to 8 threads:
But the 30mm ARP bolts will have two less threads of engagement. And if you add the washer (which I would), you are down to about 28mm of length, and only 5-6 threads of engagement:
In my testing, that was still fine at 59 ft-lbs. But as you increase the torque, the bolt's threads will strip, starting at about 80-90 ft-lbs. That's why I switched to 35mm ARP bolts, which when used with the washer, have about 33mm of shank. They protrude a little more than the Red bolts:
The Black bolts are 35mm long, so they protrude the most:
[MENTION=148218]JZiggy[/MENTION] made some measurements and ascertained that they will not bottom out even if used without the protector.
As for the torque values, I agree with the concern of someone possibly overtorquing a Black bolt at a future date. You can certainly add a label to it, but who reads labels? That is one advantage of the ARP, it can be safely torqued to 59 ft-lbs (or quite a bit more). Although I still like the smoothness of the Black bolt.