Sutsuj, I think you see this all from the perspective of a multiplayer game, where many of the problems that strike the AI, can be corrected by the human player, but are staying big problems for the AI civs. I see these problems from the perspective of a single player game, where the problems of the AI must be taken into consideration. So some features of the Flintlock mod may be working in multiplayer games, too, until now the Flintlock mod is a single player mod.
In regard to Civinator's point that stack limits are not needed to deal with stacks of doom, I mostly agree but think that you're missing three reasons that tile limits could still be very valuable:
1. Not all mods have the features you mentioned implemented, and thus it would be nice to get to import stack limits into pre-existing mods.
If such stack limits should be so nice, why are you not using the simplest solution for multiplayer games to set a limit for units in a stack between the human players ? If you play your multiplayer games with a mixture of human and AI players, you should not completely ignore the big problems the AI has with such limitations in C3C. The existing traffic problems for the AI triggered by such tile limitations were already posted above. The argument to make the maps much bigger doesn´t solve this problem, at least if you want still to have an interesting playable map for your game.
It is not only the traffic problem of the blockade of units. There are also AI pathfinding errors of units appearing, that lead to freezes of the game. The release of the mod CCM had an delay of more than one year by these problems.
What should be the solution for the production of units in a city when the tile of the city reaches the tile limit ? What units should the AI throw out of the city and on what (neighboring) tile ? These decisions can be done by the human player when having a look at the specific situation on the map and a facing opponent, but the AI ??
2. More importantly, it would be fun to have battles spread out over a larger area regardless of whether or not we can deal with doom stacks. It would be fun to be forced to do this as a human.
The battles are not "spreading out" by such a setting, as neighboring tiles are not connected in a C3C battle. Additionally in my eyes it is no fun, to handicap the AI even more with such limitations and even more it is no fun, when your game is closed by a freeze triggered by an AI path finding error.
3. Lastly, I don't know if charm works in live multiplayer, but I know from personal experience that teleport does not. Based on what I've seen, Flintlock's engine changes work in live multiplayer; specifically, I've tested that land-sea intersections work.
I cannot say if charm attack works in multiplayer games, but this has nothing to do with tile limitations.
All in all, of course it is the decision of Flintlock what to do here (and this could trigger a lot of additional work), but as the things are standing now, for me the most important would be a button to skip that option.