The Gen 2 has upgraded bolts for the subframe. If they are torqued properly then the break-out force of the pinched tubes of the subframe is probably exceeded by the bolts' shear strength.
To install the drill-through, you will be drilling through a solid section that is welded into the frame's backbone. You need to increase the existing blind hole diameter by about .10" and you have to drill halfway through the solid section, then turn around and drill through from the opposite side. In order for the bolt to pass through, the two drillings need to be almost perfectly coaxial. On some frames (I can't remember if it is the earlier or the later) that solid section is rather reduced in diameter, so there is a potential for break-through. When you are all done, you have one bolt to hold the subframe together instead of two. On paper, the joint is much stronger. In real life, you have done nothing to increase the break-out strength of the subframe's pinched ends. You've created a lot of work, a lot of chips, a lot of mess, and not gained much IMNSHO.
If you have good machine-shop skills and a decent drill motor you can probably do it without doing harm. I'm a pretty fair hand with machine shop shit and I thought it was ****ing stupid. Just keep the bolts torqued properly.
Don't get me started on footpeg bolts. Just keep them tight, too.
A general observation from a dick, not directed at you:
I don't know why people have to be told to torque bolts, and then periodically check them. I just don't. ¯\(ツ)/¯ Folks like to not do that, then complain about the poor quality of the bolts. It's a poor mechanic that blames his tools and fasteners.