No it does not. Your settlement can still be absorbed into a larger one. This is not a true statement. The guild settlement can keep their name, but the prestige still is added into the prestige for the larger settlement. The guild is part of the larger settlement even if they would prefer to be independent or maybe merge with someone else.
There is an assumption by some that players will want to be part of a guild with all that entails. There are also limits to the number of guilds you can be in. With all I am reading about the guilds, I am not sure I see much of an advantage to being in one. But that is off topic.
Personally, I still think they need to add in the protection zones. It allows new players time to expand, it lets players really decide if they want to be part of a settlement or not and it allows a settlement to decide if they want a player to join them or not. Before anyone says that is against the way the game is played, is that not exactly how guilds will work? The guild has to let you align and can kick you out if they want to also.
Anything that allows players that have spent a lot of time and energy to create a build or settlement, the ability to better control what happens to that settlement is a good thing in my opinion. I do understand the concern expressed about blank plots in cities, but since the developers are giving us the option to turn off the protection zones, players that are concerned about that do have the ability to do something about it. Will it require more cooperation in order to happen? Yes. But since the game is supposed to include building a community is this really a problem?