Exactly. Putting the 'commander' in the HQ or an assault 'Mech doesn't change the ability of your force to operate, the 'commander' isn't distracted by piloting a combat unit. In one instance you increase your vulnerability to losing a bonus from intense combat versus a fast VTOL or hidden unit wiping out the mobile HQ in one quick strike.
There's arguments in terms of gameplay for either direction, consider the difference between the King in chess, and a Queen. Arguably, the fact that you have to both protect your king in chess (and it's a piece with SEVERE vulnerability) and can lose that piece to just such an equivalent event (look up: Fool's Mate) doesn't make chess less fun to play, or less tactical, while stiking your 'commander' in the best 'mech w/best guns and gunnery certainly works better for a checkers analogy.
They're both games good enough to have made it through the centuries, but they reflect VERY different sorts of warfare. Checkers is all about annihilation, the core victory condition being only the complete destruction of all opposing forces, while Chess has a victory condition that can concievably leave the bulk of the opposing force intact, reflecting a different strategic paradigm.
Putting that bonus in a vehicle with terrible manueverability, crap armor, and almost no guns reflects a more chess-like scenario-the owner has to both defend the command post, AND press the attack. Putting that capability into the most obscenely overpowered 'mech on a side, otoh, reflects more of a checkers scenario, because while that piece may be more powerful than the others, it's still just a piece, and not necessary to the successful achievement of victory. After all, it's just another piece, just another anonymous resource.
NOT having to protect any specific asset on the board leads to a play that is all attack, all the time-which is certainly favored by some players, and could be confusing when those players are used to 'last man standing', as opposed to more sophisticated and complicated objectives.
"Last man standing" scenarios are a lot more common in the wild, because they're very visceral, but they're also the scenarios most likely to devolve into 'standing at medium range rolling die'. Those types of games often don't need nearly as much prep as people put into them, and certainly don't have a lot of room for units that aren't some combination of the best armor/firepower (two dimensions) with moderate mobility to get to that medium range RNG contest.
Put stakes on that, though-forced retreat, initiative bonuses, initiative
penalties, and it tends to shift the tenor of the table hard, and makes units you tend to overlook a LOT more useful.
