we do have a lot of information about peak-shape, all of which hints at what's going on during the overlap
But that's the problem; we *don't* have a lot of information about the underlying peak shape! They are *not* Gaussian, they usually tail. And the distribution of the tail will be different if it comes from gross overload versus silanols versus extra-column volume versus . . . We have to make assumptions, which introduce their own errors.
Just as a quick example, for a small peak after a big peak, if both peaks are Gaussian, a perpendicular drop will *underestimate* the area of the smaller peak. But if the big peak tails sufficiently, the perpendicular drop will *overestimate* the area of the smaller peak. How much tailing does it take to go from underestimating to overestimating? That depends on mechanism (and hence detailed shape) of the tailing.
If you want to get into it (and are willing to deal with eye-glazing math!), get a copy of the Dyson book and read the section on integration algorithms.