"After penetrating the second panel, the 7N6M had less energy than the 7N6, giving it less lethality"
This is not the case, since the 7N6M round has a higher hit value and a lower typicalSpeed value (meaning it retains its maximum hit potential even at lower speeds) making it more lethal than 7N6 after penetrating barriers
I've uploaded two images of the terminal hit of rhs_B_545x39_Ball (7N6) and rhs_B_545x39_7N6_Ball (7N6M) using the game's diagnostic .exe "shots" mode in a similar setup to the one you tested, with the addition of live targets before the final penetrable panel. The "shots" diagnostic mode shows truer ballistic path and speed data than the scripted trace function in vanilla Arma 3.
The vanilla tracing script has some limitations making it difficult to do direct comparisons between small separations of the wooden panels because sampling only takes place every few frames and if the projectile has travelled a certain distance. It doesn't necessarily create the sample points where the bullet has struck a surface
7N6 does seem to have slightly higher speeds after penetration than 7N6M ingame, because its initial velocity is also slightly higher. But as shown above, 7N6M still has more potential to be lethal in the above scenario.