There is always possible to make mod for a mod ) And its simple tweak.
But speaking of Mess drones, there one issue with enemies like Omega or Mess which are being split into smaller ships when destroyed, when they are on player side, combat won't end until its completely destroyed or retreated, you need either use console to force end combat or order ship with splitting mechanic to retreat, if its intact, you only can end combat via console. I'm pretty King Alfonzo won't make them recoverable just by this technical issue.
Also speaking of exploration part of mod, I think good suggestion, is make procedural generation for Mess and DomRes infested systems, like Dassault and PRV mods did for their remnant style enemies, just to have more systems with these hazards. And another idea, make ship stashes appear at random locations in mod systems, since when you found them once, you know where you can pickup alot of XIV and High Tech ships just at start of the game, since they are always spawns at same place, also these stashes are incredibly buffed in 095 because of story points, in 091 half of ships was unrecoverable due random chance of derelict being unrecoverable, so it was not that cheaty.
And about reward for destroying Mess infested nexus, its non relevant at the stage of the game when you can beat this nexus and patrolling fleets of infested Remnants, if you can beat them, its means what your fleet already strong, and have several capital ships since you need to take down Nexus and Fleets with Mess Radiants, and that unique cruiser with little quirk is just unneeded at that stage of the game. It can regen HP, but its also seems fragile too.