None of what you said actually explains how HBM could require 3x the wafers.

The base interface die has eight or 12 memory dies stacked on top of it. The wafer cost of that interface die is therefore small.

If the process of die thinning and TSV stacking reduced yields by a factor of three, nobody would consider HBM mature enough to put into production, and especially not mature enough to be increasing stack height from one generation to the next.

Trace length has approximately nothing to do with die size. If anything, designing for shorter traces means you can get away with smaller PHYs at either end.

What might go some ways toward explaining such a huge difference in die size is that the TSVs themselves take up significant die area and must be fairly numerous to carry both a large number of signal wires and all the power and ground required by the stack. But it's wildly implausible that the die area consumed by the TSVs would be significantly larger than the die area consumed by the memory arrays themselves, or that anyone would build a memory die where the memory array was not a large majority of the total die area.

If there's any truth to that ~3x higher wafer requirement for the same number of bits as compared to DDR5, it must be a combination of several factors and probably includes something non-obvious and dubious, like counting all the area of the passive interposers that go between HBM stacks and GPUs (those interposers aren't competing for the same fab space).