Firstly, I'm not sure this is generally that big of an issue, the very fact that this thread has been quiet for three months seems to speak to that. I think largely because Reapers are just as likely to hop off your server as on it. What I mean is, before the tunnel if I was at the start of a session and looked at my map table to see a level five Reaper on the map it just wasn't worth considering emissary that session unless I was in the mood for some PvP, because that level five Reaper was stuck on the server with me so when I raised a lvl 1 flag as the only emissary on the server I could be sure they'd be angling my way. Now, often I'll start a session, look at my map and see a level 5 Reaper and by the time I've turned off all my lanterns and gotten my monkey out of its box (not a euphemism) they've server hopped and I can pop my flag in peace (also not a euphemism). I've seen way more Reapers hop off my servers since the change than on. So generally, I'm okay with it.
There are two things though that I'd say. Firstly, don't put up an announcement when a level 5 Reaper arrives on a server, honestly, their egos are swollen enough already, a mighty fanfare when they hop on the server isn't going to help. Also, if I'm not emissary its just annoying, especially if they hop off again, and even if they are, I still need to scoot back to my map table to find out how long I've got. Rather, why not let pirates have a portable version of the map table map? I mean, its pretty weird that the thing is welded to the table as it is, its an existing mechanic, maybe its set to a certain pulled out level of zoom and centered on you rather than being the full thing, but that would let me scan for Reapers on my own level of wariness. I'm mostly a solo slooper and currently I'm discounting a lot of jobs on larger islands because of how long I end up needing to be away from the boat, some larger islands are viable with good sightlines, but not for Reapers, because they know I'm there they approach differently, with a map to check I'd feel more comfortable doing some of those more involved missions.
Secondly, if there is an issue its that currently the tunnel is used by three sorts of people, those actually doing the tale, Reapers, and those fleeing Reapers. It seems the best way to update it is to make the tunnel more valuable to everyone so migrating Reapers are just part of a stream of traffic, so why not make it so that on the other side of the tunnel you can idle without being lazy bearded, since it can be offline, and that you can save. The reason, I thought, against saving in SoT was that you could just save and leave in the middle of a PvP encounter. Well, you can't have PvP on the other side of the tunnels, so why not let people save their status, log off and then come back and carry on where they left off? That way you'd have more high level emissaries migrating into servers, so less need for Reapers to hop and servers kept live and interesting for longer.