Again folks understand the SEGS intro with Issue 3/4 is because the game was simple and very stable. Issue 2 had lag spikes that would literally rubber band you 500 yards.
Issue 3/4 allow respecs and have very simple requirements. Understand you would have dumpster diving, herding an entire map, no aggro cap, no damage cap - in other words blasters can nuke an entire herd.
This was the games peak time a step back to when the world was new and heroes strode through the land like gods.
As far as I know SEGS is based on Issue 3 because that's when the project started, plus or minus, and trying to support anything newer than that would have been trying to aim for a moving target for the developer(s) of SEGS, which they did not have the time or resources for. Its basically a coincidence of timing. If the project had started later, it could have easily been based on I6, or I9.
Keep in mind SEGS is a reverse-engineering project started when we were still using Brawl numbers and we barely had a good theory for accuracy. It was less a re-engineering of the servers, of which we had virtually no idea how they worked, and more a project to figure out what the client even need to run. The project didn't target I3 because of any specific love of I3 data, if for no other reason than we didn't then (and don't even now) have I3 data. SEGS was eventually going to have to make up the back end mechanics of the game because even today we do not have that data in any form except anecdotal.
However, there are certain things "baked into" Issue 3 that would be very difficult to tamper with. For example, SEGS could make Flares do I24 damage rather than I3 damage because we'd have to make that up either way. But it would be a lot harder for SEGS to make Flares activate with I24 timing than I3 timing, because the I3 client has an animation for Flares that would not be trivial to change. Well, you could change it, but to do that power-system wide for all the powers would be a lot of work. And customization would be basically impossible without essentially rewriting the client.