The only problem with running the shackle under the spring is it's harder to keep the vehicle low. You're gaining probably an inch of height that you wouldn't have otherwise.
That being said I ran the shackle under the frame on my first gen and now I'm running through the frame on my 3rd gen. No real difference in handling offroad, but definitely can feel it onroad.
I would agree with that and this is something you should consider... If super lowness is your goal through the frame with tubing and traditional shorter springs for RUFs would be better. I just went on a lowering quest and I was able to drop a good 2" from my original setup. Those short almost stock length shackles were part of that project and also helped with handling tremendously. I could drop maybe like another 3/4" if I redrilled my hanger, but with this setup I can't really get any lower. I would estimate a 4"-5" lift on my 4Runner at this time.
