I have the shell of a 69 coupe and the factory installed the torque box on top of the frame rail tab just like the first picture.
Both Dynacorn and Spectra Premium build the inner part of the front torque boxes narrower than the cp/fb. They simply aren't wide enough to mate to that tab as the second picture shows. The real question is whether Ford intended the firewall alone to tie those two pieces together there or whether there is supposed to be a doubler that fits behind the tab and the inner tb?
Sure- The inner, upper edge should be below the flange on the frame rail, not above it.
looks like you changed the picture. based on what i'm looking at in the picture you linked from someone else's work (and pictures from Aolshove), it appears they may have bridged the gap with a weld. so in reality the torque box someone else installed probably isn't underneath the frame rail the way you claim mine should have been (and incorrectly installed....). i'm guessing you don't have a better picture.
looking at photos posted by Aolshove, it appears the aftermarket convert torque box comes up a little short just as the op describes.
in reality, whether a person welds it on top like original or underneath (or simply bridge the gap with a weld) it probably doesn't matter since you can't see it anyways. at most you would have to push the toe panel/firewall down the thickness of the original torque box in order to attach it to the frame rail if you put it underneath. that gap is in the noise though.