Way back in Civ V days when 1UPT and SOD were first being debated I proposed that the solution to the Stack was a realistic Supply Rule. Being a military historian, I can quote numerous instances where concentrating an army was absolutely dependent on supply available, and other instances where armies were forced to disperse because there simply wasn't enough to feed them all in any one place. Transport those effects into the game, and a stack/concentration of units becomes something you can only do after preparing for it, and a stack without such preparation is Doomed, not Doom.
Today I would argue for a tactical battle lay-out along the lines that the Humankind game is showing, but that makes penalties for concentration of forces no less important, because a large army of units in that form is just as unstoppable as the old SOD.
The fact that the entire Supply Line mechanic and effect can be 'invisibly' calculated by the computer for us so that a relatively few rules about effects and consequences are all the gamer has to deal with make it, IMHO, even more important to include some form of Supply mechanism in Civ VII.
As an aside, some Great Generals were notoriously good at keeping their troops supplied, so bonuses connected to some of the Great Generals regarding Supply (extending the length of supply lines, or where they can be traced from, or what terrain they can be traced over - lots of possibilities) would be appropriate and another 'Civ Peculiar' part of the game (because Humankind has NO Great Generals, so individual-inspired mechanics are missing there)
Being that warfare is such a big element of Civ type games, I really think that game designers should listen more to military historians like you. Unfortunately, they don't.
There are other ways to make stack of doom less intimidating to players.
Stack of doom is scary also because cities conquered by the enemies are subjected to atrocities that will make rebuilding them very time consuming. Imagine having one of your mega metropolis that globally ranks number one in hammer production razed to the ground by an enemy army. That can be very demoralizing.
Moreover, if the mega metropolis has a population of 9, and the enemy army that marched right into that city has only two badly damaged units, its simply out of touch with reality to think that they will be able to carry out destruction as extreme as razing it to the ground.
I propose that armies which successfully capture an enemy city needs to continually be supplied from the home country until the entire city is subjugated. Subjugation might take several turns. The number of turns depends on a variety of factors. If the city conquered followed a faith that is very different from the faith followed by the home empire of the conquering army, subjugation period might increase in length. If the occupying army commits atrocities, such as razing cities, or killing the population, the subjugation will lengthen very dramatically. If the conquering army uses archers and swordsmen while the conquered cities are already in the internet era, subjugation period will take VERY LONG. If the conquered city has a population of 14, and the conquering army has only two badly damaged units, subjugation period will also take a long time. Great generals upgrade might contain abilities which decrease subjugation length.
If the army still needs to be supplied from the home empire during subjugation period, the supply line issue still exists for the conquering army. In another word, if the supply line is intercepted, the conquering army will continue to suffer attrition, and that will make them vulnerable to counter attack.
Therefore the occupying army has all the incentive in the world to "play nice" with the cities they conquered. Otherwise, they can't bring the occupied ciites under subjugation. Without successful subjugation, the conquering army will be reliant on supply from home empire. They won't be able to get supply from the cities they have conquered. As a result, the home empire will have to keep bearing the huge increase in maintenance cost, which, in my proposal, includes supply line cost.
If the occupying army has all the incentives in the world to play nice with their conquered subjects, we players are more confident that the cities that we lost to the enemies will not be so badly damaged during foreign occupation period. Moreover, since the occupying army needs several turns for subjugation, we still have a chance to destroy and kick the enemy out by intercepting their supply line. This is just another throng in making stack of doom less intimidating to players.
Furthermore, if the occupying army has a long supply line connecting its home empire to the city that it has conquered, I don't necessarily need to intercept the supply line on the very hex adjacent to the conquered city. I can intercept that supply line six or seven hex away. THat means that the occupying army now has to move its units out of the occupied city to fight my own military units that is intercepting its supply line. The more units redeployed to restore its supply line, the less units available to stay inside the conquered city. The less units available to guard the conquered city, the bigger the difference between the size of the city's population and the size of the occupying army. The bigger that gap is, the longer the subjugation period.