The server merge rule used to be No other ships on the server then you would merge when you dropped the anchor, but only when anchored. They removed the anchor restriction first because people were exploiting that, never anchor and eventually you would be playing single player SoT. I got a 2 ships on a server once with a friend. He was afraid to alliance in case one of us got boarded he didn't want the hostile ship to know each others location. So I was like ok well we should be fine as long as we stay on the server and it doesn't get down to last boat standing. I was at plunder outpost he was up at galleons. We started playing and he was merged off the server.
I have also tried hiding off in the roar doing commendations since people rarely go out there. Get merged often to find now there's ships near me. It seems like there are a few rules now looks like if you are far from other ships you are ruining the social experience Rare wants for the PvP crews so not sure if its zone specific or a distance between you and the closest ship but it will merge you if you're being anti social because you're ruining PvPers fun. They had mentioned something in the past about wanting to do something if a crew keeps getting repeatedly sunk by the same crew. Seems like they might have added a rule for this.
Hard to know exactly what they are now. I believe the game will not merge you if you are next to other ships though. Like if you are actively engaged. So perhaps where you spawned was far enough from the other crews or it saw they sunk you multiple times or a combination of those factors?
a few certain rules
-You will never merge if you are in an alliance as the merge system wont break alliances and it cant merge 2 ships at once.
-The whole crew needs to be onboard to merge... Though there might be a small radius around the ship I think I merged once while in the water right at the ladder. But usually the mergers have happened for me either while climbing the ladder or the second I got on deck.
So ironically they merge you to force player encounters with other crews for the rare chance there is a fun and enjoyable ship to ship encounter. But they will also merge you if you get sunk too much?
Considering PvPers are using the pirates life portals to exploit merging to a new server with a grade 4 flag to find emissaries to hunt down with a full stocked ship I wish they would just give us the option to merge rather than having it just be a seemingly random thing