I've considered all those options, trust me, I love the Commando, but it just isn't in scale, when FD drew it up for PGI he imagined it probably being larger than it is in-game.
Allow me to demonstrate:
Here is your pilot in the in-game COmmando cockpit:
Now lets just put it in the Commando head shall we?
Oh {Scrap}! It doesn't fit! This isn't surprising, none of the mech cockpits do (except for the Raven sort of), since the in-game mech cockpits are horribly blown up, with a fish eye effect, if they weren't you wouldn't be able to see anything out of your mechs viewport since most of them are actually pretty small when you look at them in actual scale, I like to handwave this away as; you're just seeing an enhanced composite image of your cockpit viewport through your neurohelm, hence the fish eye view and why they appear larger than they actually are on the model itself.
Ok so, the pilot is in the exact pose he is in-game, so lets just remove the in-game cockpit and he should fit in the head right?
Nope, as you can see, his arm sticks out of the side of it's head, now, sure I could just move his arm but we're trying to stick with what is in-game now remember? Lets see how his legs fit...
Well, he fits....well...not really, he's high enough that he'd be warm and toasty above the ammo loader, engine and it's heatsinks, BUT, he's in the way of the mechs arm actuator joint and the myomer muscles that would come out of it! The red circle is how the entire joint is on the model itself, and no, there isn't enough space for it to pass underneath him, he's practically sitting right next to it, on top of the fact that I had to remove the Commando's neck for him to even fit in the first place.
Well, we can just move him a little to the side right and it'll be fine right?
Nope.
Completely blocked by the eye sensor, which as you can see from the in-game cockpit, it extends past the cockpit, so you can't fit there, not to mention he wouldn't even be facing the viewport.
Lets just rescale the Commando then!
Unfortunately that doesn't work either, as the Commando's neck still completely blocks his feet.
Commando is just broke, only way to get the pilot to fit in there would be to resize it to a size that would be too big for a light, or to have the pilot sit higher up in the head, but then he wouldn't be able to see out the Commando like he does in-game!
Of course, this could all be fixed, by taking the lore friendly option of just saying that the pilot doesn't even use the viewport as he has a compressed 360 degree view through his neurohelm, unobstructed by anything and not requiring him to look through the tiny viewport. But of course, the game isn't like that, as I'm sure you know.
tl;dr pilot doesn't fit in the Commando.