@FlipAllTheTables, who doesn’t have enough activity time in the game recently to post a direct reply, sent me a DM with their thoughts. I am quoting them verbatim here.
To go more indepth, to attempt to compensate for the fact APHE rounds deal damage with the explosion Gaijin gives APHE rounds a generally weaker armor spall preset, meaning that the spall created by armor penetration itself when using APHE rounds is of lower amount and less damaging when compared to solid shot rounds. Gaijin’s proposal was that if explosion spall got nerfed by limiting it into designated sections, the spall from armor penetration would be buffed to match solid shot rounds.
Armor spall presets example
This is the armor spall preset that is used for 90mm M82 APCBC-HE, which you can see in the “secondaryShattersPreset” section.

In comparison, 90mm T33 APBC and other solid shot rounds above a caliber of I believe 20mm use the “ap_large_caliber” preset.

This preset applies only to spall generated from the armor during penetration, and the “ap” preset generally produces less spall that also deals less damage individually.
This code comes from the DEV server where you could test the APHE changes using protection analysis, and toggle the new damage on and off. Again this is for 90mm M82. This “testProperties” section is large and contains basically everything from the change in the armor spall preset change to the actual sectioning of the explosion spall cones.
As you can see, when the “testProperties” were toggled on the armor spall preset of M82 was changed to match that of T33.
However since the spall cone nerfs did not happen, this buff to armor spall didn’t either. The only buff that APHE did receive was the “warhead integrity” buff where if an APHE round has sufficiently little TNT in its composition the nose of the shot body will continue traveling forward after the explosion.
Transmissions and Engines are just absurdly weak for some reason, they die from the smallest fragments. Even crew have a higher survivability that the average warthunder transmission.
Additionally, I answered them with the following message:
Hey mate. Nice hearing from you. I will post your reply to the thread later when I’m at my pc, verbatim of course.
I do think something changed specifically in relation to transmission and engine damage though. I can’t remember when it was, but after one update it became really noticeable - you would shoot someone in the turret from the frontal aspect and in the back their engine would die. Do you remember what update this was by any chance?
To which they replied:
Nope, it’s one of those things that just short of appeared, and even going through the datamines on it makes little sense as from what I can tell the hitpoints of the actual transmission and engine modules only went up, not down. I could be looking at the wrong thing, but it could also just be an outright bug. Again, “even crew have a higher survivability than the average warthunder transmission”, and that’s not an exaggeration, I’ve seen plenty of cupola shots where some crew take multiple fragments and live compared to the transmission shaft taking a single one and destroying itself.
I do have the inkling memory that it’s something that came quite a bit after the proposed APHE changes though, it feels far more recent.