I think you are going less against the current than you say. You are of course right, a better player should win. But the questions are:
How big a difference in skill level is required to win 100% of games?
Which skills in the game matter the most?
The first question is important because not all (or even a sizeable minority) of Civ games take place in a 1v1 mirrored map. There is a lot of randomness involved. You want there to be some uncertainty in the outcome. A tiny difference in advantage (from skill or luck) at the start of the game leads to a bigger difference in power at the end of the game. The important thing is how much this difference increases by. If it is too small, then early skill (or the map) doesn't matter enough. If it's too big, the game is decided way before the end, and we never get to see the late game. From your description, Civ4 hit the sweet spot in the case of closely matched players, probably in part because of the very mechanics you describe. But most people who play Civ don't want to find human players that are close enough to their skill level and play an entire game on quick speed in one sitting. They want to play epic/marathon, in their own time, vs an AI. This AI's 'skill' can be tuned via difficulty levels, but it can never be fine grained enough to match the player exactly. Furthermore, the randomness inherent to the game makes such exact matching of early advantage impossible in practice. So we need the threshold at which early game advantage translates to automatic win to be significantly higher. Not disappear altogether, but be higher. This is done by reducing snowballing.
The second question also comes into this. With steep snowballing, early game skills matter the most because no level of skill later on in the game can ever catch up. This makes the late game not matter and kills ton of the interesting features that Civ has. Again, we don't want late game skills to overpower early game skills, just to balance it. If nothing else it kills replayability if your initial build order makes-or-breaks the game more than anything else.
You bring good points, which ultimately lead to the fact that different players like different kinds of games and it's impossible to please anyone.
regarding the "early game optimization vs late game optimization", the argument is ill-defined. by the time one has a bigger empire with twice as much production of everything, then he has won and there's no realistic way to get back, save for intentional suicide of the stronger player. in that case, late game decisions are really made irrelevant. however, if better early game decisions lead to a 20% more production of everything, there is still enough margin to recover. And among players of similar skills, that's the kind of differences that are usually to be expected.
I admit I am not much of an expert of Civ6 balance; I have a much greater experience with civ4. So I don't know how skewed is the civ6 balance. but here are a few things about snowballling that most of us can agree
1) if snowballling comes from MUCH better play, then it is not a problem, and in fact it should stay there.
2) the treshold for snowballing should be high enough that random factors like starting location do not automatically translate to a victory. it should also be low enough that consistently good decisions can snowball in the face of consistently acceptable decisions
3) great differences among players should snowball. Small differences should equalize.
I think the most important point is 3). To address it, I think flat bonuses are the best way. in the case of civ4, it was a tech bonus up to 20% if you lagged behind in tech; that way, with a small difference in research you coul still stay close to the lead. they'd be a few turns ahead, and with skill they could use that to their advantage, but it certainly wasn't an auto-win. but if someone had a tech advantage greater than 20% over everyone else, he'd keep on growing. Good thing: small advantage is equalized, past a certain point it snowballs. Same for war, you needed 20% to 80% more army than the other guy to kill him, depending on terrain, promotions and somesuch. Good thing; a slightly greater army can give you more room to try manuevers, like sending some of it to your alllies on the other side or embarking some of it and trying to open a second front, but it does not guarantee victory, while an overwhelmingly bigger army is an insta-win button.
As long as those checks are in place and balanced reasonably well, snowballing is a healty mechanic.