That's an extremely good point. Even when it comes to comparing round bullets energy is a very rough approximation. A larger, heavier ball is going to have more energy and more momentum, but it needs to punch a much larger hole to penetrate. This is another one of the problems with some of the tables in Williams' book. The one on page 928 which gets posted to internet forums a lot in particular had its numbers extrapolated from experiments against a 2mm mild steel plate, so it didn't actually involve shooting at 3mm or 4 mm of armor and it relies on assuming that bullets of different calibers behave similarly with the same amount of energy.
https://journals.lib.unb.ca/index.ph...ew/17669/22312
Here's the English summary of Peter Krenn's tests, which Williams also relied on heavily for his information. It's still not clearly explained how they came up with their various charges, but if you go through and calculate the various kinetic energies at both 30m and 100m you can find quite a few places where the energy and penetration of mild steel don't match up with Williams' table. You can even find places where the penetration of mild steel doesn't match up with the penetration of wood for the same energy.