Ahoy maties!
I've seen many concerns and issues about the Skeletons Ships raised here and elsewhere so I tried to gather as much information as possible to answer several of our questions.
Given that the answers are a bit scattered across several posts on Reddit, I decided to summarize all that and list the official responses below for readability. This way if you prefer to read the official answers, check the links :)
Why the Skeleton Ships are not an emergent encounter like Meg?
The Skeleton Ships were first introduced into the game as per a Skull Fort style with a Cloud signaling in which corner they are. Those are meant to be difficult encounters with many waves as we've experienced during the Cursed Sails campaign.
However, Skeleton Crews will be fighting soon also in different ways as Rare is currently working on extending these into more emergent encounters in the world. Skeleton Ship spawn points will vary around the world soon and won't be just the fixed encounters in the corners of the map we're challenged with right now. Those emergent encounters will exist in addition to the battles and will be more tailored to our crew.
Finally, the Meganesque aggressive style of encounter is only one of them and one can wonder what could be the others!
Why a Skull Fort is never active at the same time as a Skeleton Ship Battle?
Some of you probably remember during the Cursed Sails campaign that some servers didn't spawn animals or other AI in the world. It's because the Skeleton Ship Battles and the Skeleton Forts are pretty intensive on the server performance and Rare allocates a large pool of their AI budget on it.
Of course, when no one is in the area, only the cloud is visible and the ships aren't spawning. It's the same for animals, skeletons and other AI. However when someone go there, the server has to allocate budget for this. If they were two encounters active simultaneously, this could cause some issues for other crews who are looking for chicken or fighting skeletons. Sea of Thieves is a shared world and many activities can go on in the same world so the server has to manage all the systems and all crews actions across the entire world. This limitation makes sure that the server performance won't drop below a certain level and will not affect the players.
On the other hand, Rare is aware that some players really want to push forts so they are currently doing some work to improve how they schedule every encounters. If no one is engaging with one encounter, then they will change things up and activate another one.
As this answer is very technical, I tried to summarize as best as I could and I recommend you consult the official answers below.
Skeleton Ships and Server Migrations
While this one is probably the biggest issue currently with the Skeleton Ships, be sure that Rare is aware of it and they are working on it!
They know that they shouldn't allow migration when you are in proximity of a Skeleton Ship Battle just like their approach to Skeleton Forts. They will prevent server migrations in a much wider zone around these ship encounters allowing us more space to move and restock without migrating.
However, when the encounter finishes, a migration could happen even if the treasure is still in the water. Rare will ensure the loot will move with you and is fully interactible.
Why the Stronghold items do not only spawn on the last sunken Skeleton Ship?
The Stronghold items only spawn with the captain's ship which can be identified in the last wave by the red name above the captain and its different sails from other ships. However it is not always easy to identify it in the middle of the battle and it happens that this ship sinks first and that the Stronghold items are easily lost.
Rare understand the confusion as it is inconcistent with how the Skull Fort encounters end when the captain is defeated. They are currently reviewing this and see how they can improve it.
Source: 1
Why the Skeleton Ships Battles are not in Order of Souls quests?
Rare initially considered these but as they are expensive entities on the server performance they couldn't support the cases where multiple crews triggered an Order of Souls Skeleton Ship battle. However, clever emergent encounters are on the way and will allow all players to fight in good condition these Skeleton Ships.
Source: 1
I hope it will help you to see more clearly until Rare reveals in a more global way the improvements and bugs on which they are currently working.
If you still have questions that have not been answered, feel free to ask them in the replies and I will try to see if I can find anything on it.
Cheers all!