Even though that did happen in history I don't think the English or the Spanish ever set out to establish all their colonies with the hopes that one day they would become independent.Well, colonies in reality are meant to become independent/merge into new states. Thing is, you should be able to get MASSIVE benefits from them, in a more or less short period of time. And don't forget that in my system, some colonies could stay yours a long time, provided you have fast access to them, it being by high porosity land vs. low porosity in the other side (where another civ is, I'm thinking about mountains ranges, lakes or even big rivers, or hills, forest/jungle, deserts... the possibilities are numerous for creating a "natural craddle for your civ"), not talking about roads that would dramatically improve the porosity with your colonies, basically making no resistance vs. even high porosity lands. So I think the trade routes roads system of Civ6 would quite be nice as to decide where to send your traders. In that perspective, if you put enough work/attention to your colonies, they wouldn't even be "colonies" so to speak, they would just be part of your empire permanently.
That being said there are "colonies" that still exist today, or at least dependent territories, so I don't think automatic separation eventually should be a thing. But I do agree that it would be something that these cities would have to work towards.