A disclaimer; I'm an experienced player, I know how to handle losing everything in this game, and do not need anyone telling me I need to "get good". I originally sent this as feedback to the SoT-support, and they asked me to post it here. So here goes..
I definitely see the appeal of leaving this Tall Tale bug in, and I absolutely think a version of this feature should be in the game. As it is now however, it does not work. Having a lvl 5 reaper server-hop to your server is not fair to the emissary ships who have been playing on the server. When that ship spawns in without any warning, that's a huge advantage to the reaper, and disadvantage for the other emissaries. I've been playing for a few hours today, as a reaper, and to my crew it wasn't really an issue beyond the fact that there was suddenly a lvl 5 reaper right behind us. The fact that they've also brought with them a lot of supplies, and no loot obviously, leaves us at a disadvantage. They have nothing to lose, and we have everything. Now this is bad enough - but when another Reaper server-hops to the same server, it gets exceptionally worse. When a fully leveled Reaper who can see every active emissary comes into the server and starts sinking emissaries who weren't aware of them spawning in, that's not a good thing. This isn't sustainable gameplay, it's not fair to the player-base as a whole, and to me it looks a lot like an exploit.
My crew is experienced, and we've learned how to lose in this game. This time we sold most of our stuff, and made sure they didn't sell any of ours. I just don't appreciate being ambushed by a fully leveled Reaper when we've already fended of several other server-hoppers and finally just wanted to end the session. Not generally the feeling you want to feel at the end of a gaming session.
I'm also thinking of new or inexperienced players. This game is complicated and confusing, and I honestly don't think features like this makes it easier for them. I want new players to stay! My crew avoid sinking them, we help them, and we only sink them if they attack first.
The emissary system is supposed to be risk and reward, but on equal ground - so when the reapers are given such a huge advantage over other emissaries that's just incredibly unbalanced. It needs to be changed, it needs to be nerfed. Why would I take the risk of putting on an Athena emissary, go to a Fort of Fortune, only for a level 5 Reaper to server hop in? We always pay attention to leveling reapers, but with the server hopping that doesn't cut it anymore. I want to be aware of the risk before I do that - and the server hopping removes that certainty. How does this encourage players to use the emissary system? Because to me, it doesn't seem like it does.
TLDR: It's very unbalanced that my crew had to run away from two separate server hopping Reaper galleons just to sell, after having sank 2 other ones in the very same session, when we're careful and experienced at the game. It needs to change.