I think it depends on your definition of 'different game'. Don't get me wrong - I understand the principle of what you're asking; and I will do my best to provide a level of targeted reply. It's something I've pondered, myself, from time to time - as an avid/active modder of the game who is reasonably familiar with the structure and how it all stitches together. I will say - I have no knowledge of the points-of-reference you cited: neither Auto Chess, nor Dota 2, nor even Warcraft 3.
For a question like this, I think it's important to boil down the game to its core components. The game itself consists of the game engine, which I would describe as very much 'hard-coded'. That game engine is designed to enable a turn-based, 4X game, based on a tiled map made up of hexagons. There's no getting away from that core concept.
There are then the layers of 'game information', 'specific gameplay experience' and 'scripted behaviour'. Broadly speaking, I consider the first to be the UI, the second to be the (static, but modifiable) database and artwork (both 2D and 3D) and the third to be the more dynamic, Lua-driven evaluations and changes to instances of items in the game.
In essence, each of these layers is highly moddable. With enough effort and imagination, you could make a completely different turn-based, 4X game based in a tiled map made up hexagons. In terms of player interaction with the game, you probably need to accept that you're stuck with concepts that are the equivalents of players, units, cities, improvements, buildings and suchlike. Of course, you can heavily reimagine them - but I am specifically referring to the interaction between these elements. The game will be based around having multiple players, sharing the map, interacting with each other ('diplomacy', but also in other ways on the map), using 'units', founding 'cities' building 'improvements' and/or 'buildings' and so on. Generally, the player will collect 'yields' to make progress and have different things locked behind certain milestones (e.g. 'technologies' and 'civics') and there is also a general idea of 'time passing'.
Of course, these are all concepts that are the basic building blocks of the Civilization series. From a reimagining/re-theming perspective, it is all up-for-grabs.
When I was early in my learning-to-mod journey, I pondered whether I could make a purely exploration-based game, set in space, for example - where 'yields' were 'matter, where 'cities' were actually 'stars', 'improvements' were actually 'planets' and so on. The simple answer: this would be possible. Would it make a good game? Probably not. But the point here is that it could be done, if one wished. How much of that is worth doing before you are better off making your own game with its own engine is also debatable.
In my considered opinion, the sensible limit to mod the game from the ground-up is probably an entire re-theme. Of course, there are many enterprising modders who have bolted on 'new things' within the existing theme - which proves the power of what is possible. But at the point you do both a complete re-theme and start to implement brand-new mechanics, you're going into 'new game' territory so much that I think the better investment of time is to, well, make a new game from scratch.
