TL;DR: implement micro-services to handle data and instance-based architecture for the core game. Simply, "merging the servers" would cause many conflicts, it could be done, but would probably take some time to do. From Sega's business standpoint, it wouldn't make much of a difference anyway (they probably only pay for the data throughput on their servers, so fewer players playing means less data, means fewer bills to pay), so that's why it will most likely not happen. Your solution would just be doing a server transfer to another ship.
This happened with Black Desert Online. The solution is similar to what BloodyKyona mentioned. Currently, with PSO2's architecture, the solution won't work with a rehaul on player matchmaking as it is only server-based and not player-instanced-based. Yes, the arena and CM blocks allow for cross-server, but it's probably messy code and doesn't support all the data; there will also be many conflicts. If NGS is following PSO2's core server architecture it would need a full revision in order to achieve what some MMOs have done. As I mentioned with Black Desert Online, the devs consolidated all region servers into 1 continent server (per continent), but each server has multiple channels. The special part is, there are server events, and although every player is on a different channel and a world boss appears, everyone can fight the boss in different channels and the HP is shared across the whole server. In architecture, this is the bubble-up method. If Sega wants to create an upper level to encapsulate their servers and then have super servers, it could work, but it would be a bit messy since it isn't a planned-out thing.
If Sega was serious about this. An example. Sega can have 1 master database for account data, all the important things. Another database for NGS data and 1 for vanilla PSO2. Of course, proper Cron jobs will be in place and etc. They probably have some micro-service architecture in-place... So now instead of having individual servers to log in to. The servers can be regional somewhat for better ping or lag, but tbh the data center infrastructure these days is very good so there is no need for regional or servers like that.
I think, ultimately, the reason we have these ship transfers and whatnot, is because Sega knowingly created this dilemma so players could play the market or ship transfer when in reality, it's just probably changing a flag in the database to allow that server to ship the character is on lol.
Back to the solution, Sega can make it all instance-based. 1 reason for multiple ships is maybe they use 1 master database per ship, which starts to become costly with more load. What I think Sega can do, is probably have a queue system for data managed by clusters that later parse the data to the main database with multiple replicas. So, an account has many characters but is no longer tied to any server ship. Using micro-service with instance-based architecture. A player can join a channel, which will be created based on server status. Do you know the auto-scaling feature?
1 Server > Channel 1, Channel 2.
Let's say Channel 1 and Channel 2 are both at 50% capacity. Channel 3 gets created and a player can connect to it. We can use the pub-sub technique for routing data in-between. Now, let's say that so many players are coming on and we reach Channel 50 on the 1 mega server, and the server is overloaded? Then Sega would have to turn on another server? Not really. If Sega can separate many core functions into its own instance, and always replicate and create a new server node in a cluster, then scaling doesn't become an issue. The real issue is going to be the load capacity. I think solving load capacity, is only about upgrading hardware at the moment, which is also costly. Like Genshin Impact, iirc, spends almost $200m USD a year to keep their game up and running (apparently...)
Here is a better explanation, it is kind of what I'm trying to explain: https://core.ac.uk/download/pdf/231161154.pdf
FYI, this is also a big issue with BlockChain technology, look at the Ethereum network and the proposed Layer 2 solution. This isn't something that will be solved that fast but could give an idea of how to have a possible solution.
I forgot to add, that actually doing and creating this architecture I describe is also very costly. Unless PSO2 and NGS is making Sega over maybe $400mil a year (and consistently), it's not worth implementing, even if the game is F2P. Do you get it?