Here I go again...
Being a military historian, and having plowed through this subject in the context of Civ V a couple of years ago, here's my take:
The ability to concentrate troops in a meaningful way has always been dependent on two things:
Command and Control
Supply
We can use Either or, better in my opinion, Both to provide 'limited stacking' (concentration) for Civ VI (or, more likely, Civ VII).
First, Command and Control. In the Ancient Era there was very little of either. The largest permanent units that have appeared in any of the (admittedly sparse) ancient texts are between about 300 and 700 men, and can be either all one type (archers, spearmen, 'warriors' with clubs, maces, short swords, knifes, javelins, etc) or a mixture, usually of what the game calls Melee/Anti-Cav (warriors or spearmen) and Ranged troops. Above that, nothing. That means that anything resembling an 'Army' of several thousand men is virtually uncontrollable. About the most sophisticated maneuver possible is 'Follow Me!' with a bright banner flying above your chariot so they can see who you are. In most battle depictions (again, very sparse and frequently propagandistic in tone) it appears that most of the fighting is done by a few 'Great Men' leaders while everyone else tries to stay out of the way. Homer's depiction of Dark Age Greek warfare in the Iliad is the same: a few Great Men do the fighting, the rest are, literally, 'spear-carriers' conspicuously unimportant to the outcome.
By the Classical Era you start to get more 'general' organized units: the Greek Phalanx seems to have been divided into line and file that were the same, so the 'standard' 8 rank-deep Phalanx had 'companies' of 8x8 or 64 men. Alexander's 16-rank deep Pezhetairoi pikemen had 16x16 units of 256 men as the basic unit. 6 - 8 of these were combined into Taxeis of about 1600 - 2000 men - the earliest 'Regiments' on a permanent basis, identified by their commanders' names and apparently recruited by region in Macedonia. A little later the earliest Roman Legion appears to have been a decimal organization of 100-man Centuries organized into larger Cohortes and Manipulares. The Persian Immortals were originally 10,000 strong, which implies another Decimal organization of 10 x 1000 man units, each of 10 x 100 man 'companies'.
And so on through the Eras. Development of larger, permanent military organizations, in fact, was sometimes much more important than any development in weapons technology. One Major Component of the Mongols' success was that they were organized into ferociously-disciplined units of 10, 100, 1000, and 10,000 man Tumens that could be maneuvered at will by audible or visual signals. Against a medieval European army that still maneuvered by 'Follow the guy with the biggest banner', this was a devastating advantage.
Second, Supply. The only way to send food to an army was by boat. Anywhere you couldn't send a boat, the army ate off the surrounding countryside or carried everything with it, which meant it could eat for a week or so and then started starving. No Army marched through Tundra before the Industrial or Modern Eras, because it could not be fed there. Very few tried to march through Desert, and when they did it frequently ended in Disaster (see Alexander the Great's march through the Gedrosian desert for a nasty and vivid example). That means some terrain will be virtually impossible to stack in unless you are next to a river or coast where boats can supply the units there. Even with roads, before railroads wagons, carts and pack animals could only extend a 'supply line' for about 200 kilometers or so, less in rough terrain, desert, jungle, tundra or marsh. Once you have modern roads/trucks or railroads, and modern powered shipping, virtually any number of units can be stacked and supplied anywhere, if you are willing to pay the price in Infrastructure. Notoriously, in WWII the USA, which was supplying troops in all parts of the world from Europe to the Pacific Islands, had upwards of 40,000 men in 'rear services' for every 10,000 Combat Troops. In game terms, that's a Supply Cost per turn approximately twice to four times the Maintenance Cost of the unit itself. Think twice before sending your Army far, far away!
So, to do a quick summary:
Stacking will vary enormously due to supply technologies and Command and Control technologies and techniques. This can, to some extent, be 'built in' by Era; for example, a Basic Stacking Limit might be:
Ancient Era:...................2 units
Classical Era:.................3 units
Medieval Era and later...4 units
Modified by Civics or Technologies that allow you to form multi-unit Corps (Industrial Era, historically) and Armies, and effects of Great Generals, which should definitely allow higher stacking levels in all Eras.
We could even include specific Units as multi-unit 'stacks', so that the Romans get the advantage (in the Classical Era) of a Roman Legion consisting of 2 Swordsmen which form one unit for stacking purposes, or, in the Atomic Era, the proper Military Civic might allow the formation of an Armored or Panzer Division consisting of one tank and one (motorized) infantry unit as a single unit for stacking with special combat bonuses for 'tactical combined arms'.
Support Units should be redesigned to include exclusively those 'non-combat' (military engineers, medics, supply convoys) units that enhance Combat Abilities or other unit attributes, but Never have any sort of Combat Factor themselves. BUT, because they represent extra 'tail', they would count towards Stacking - more mouths to feed within the same Tile, more elements to control within the same force. The development of Army Staffs in the Industrial Era will make a huge difference in Stacking Limits' by the way, especially including the stacking of Support Units.