Yeah, the breached locations not working in a vacuum is a pretty big simplification, and the game doesnt care about atmosphere changes so its all odd. Like, you can take hits in normal atmo, no need to roll breach and you are safe to go under water. But underwater or in a vacuum, now you need to roll breach checks. Most of the time you dont transition, but it does come up, and the abstraction's rough edges is noticeable.
As for shockwaves, I think scale is where the Cannonshop breakdown stops working. Like, yes not a lot of momentum is transferred when mechs take external damage, as you need 20 points and a fall to shake up the pilot enough that they take 1 point of damage, but the momentum ammo explosion theory does 2 damage to mechwarriors with no mitigating roll to avoid it. But im ok with that, and dont see a problem. Small internal explosions are just way more terrifying then external ones, so it makes perfect sense that a 20 point internal ammo explosion does worse things to a pilot then 20 points of external ammo explosion.
As for the barrier effect, its not gonna do much. You get concussed as your brain gets rattled despite the skull barrier, and its held in place pretty tightly in your skull. Likewise, you shake a mech with some serious Gs, the pilot is gonna get tossed around and battered, even strapped in. Even 1-2 internal tank rounds are enough to send tank turrets flying when hit, despite the turret NOT flying off when struck by the same rounds externally. The mech getting tossed from an internal explosion and bumping the pilot into all manner of stuff and sending shockwaves through the mech as it expands and contracts during an internal explosion sound really plausible, way more so then electrical feedback.
As for the ammo explosion damage not mattering for pilot damage, I just take that as part of the game abstraction. Yes, the internal explosion of mgun ammo is worse then the internal explosion of a gauss rifle, but that is mostly handled by the damage transferring to the CT and vaporizing the mech. Ammo contained by CASE? Well, your pilot lives, but battered, as most of the damage goes out the back. Ammo not contained by case? Well, if the ammo explosion is big enough, and you dont have auto eject, your pilot, along with every other component on the mech, is dead once the internal CT hits 0 from that AE ammo explosion. So yeah, mgun explosions DO result in more pilot hits if not prevented by case, while a big mech with a lot of weight to resist momentum can more or less shrug off one gauss explosion (it doesnt core out the CT unless most of the mech is already missing), while a hollander turns the pilot (who didnt auto eject) into paste when it explodes and has more then enough damage to core the CT and make the whole mech a crater, modern tank style.
EDIT: I was picturing the scene in terminator 2 when the grenade goes off in the t1000 and splits him in half, which does way more damage/stagger to the t1000 then anything else in the movie so far, outside the freezing/shattering gimmick. Thats what I picture happens to a mech, like if you didnt have CASE and get that internal explosion, well now your torso and arm are flying away and your mech is all bent/warped, with the head practically upside down and pilot just dead (again, judging from t1000). The no salvage thing from internal ammo explosions that are big enough to crack the CT I always liked.