I would think it could still be effective with the welds on the back but obviously not for planishing directly over the weld . The high spots where his disk would be is away from the weld seam. I equate the situation to pushing down on one of those flimsy hoods with little to no support on the bottom. You push one area down and another raises. Ideally you'd want to raise that low to fix it, which in itself will lower the adjacent high spot . In this situation, you consider backside access before welding and keep it cool where you can't address it, but with two people there's a lot of areas you can address as long as the guy inside the car has a nice pillow and ear muffs. Stretching those seams would be the first thing I'd do, not shrink, then I'd block the metal and planish from there. Then again, we're talking behind a quarter with access issues on the back side.
the process of using a shrinking disk right around the seam is only tightening things up around the sunken in weld area. In other words, you're just smoothing out the contour but loosing radius. If it's possible to stretch the weld seam it will release some tension pushing the metal up , and that alone would help some of the perceived stretch and you'd be able to get the proper contour/less bondo. Without access to the seam or a helper you can use a stud gun and wrestle with pulling the shrunk up. It won't properly stretch the metal but if you're hitting your highs down while pulling you are somewhat planishing the metal. I would do that after blocking as well to show me where to hit while I pull up the shrink.