Okay It works fine if comment out these lines in M28Overseer.lua.

    elseif not(bApplyM28AI) and oBrain.M28AI then
        --oBrain.M28AI = false
        --oBrain.M28Team = nil
        --M28Team.CreateNewTeam(oBrain)
        if bDebugMessages == true then LOG(sFunctionRef..': No longer applying M28AI to brain '..oBrain.Nickname..'; assigned it to the team '..(oBrain.M28Team or 'nil')) end
    end

(2112 - 2114 lines in version 157 from git)

log with enabled debug: https://pastebin.com/yKHa4hbH
log with enabled debug (after comment out): https://pastebin.com/nNqUA4ME

I don't quite understand the logic structure itself, but it seems to be designed for an individual AI player, and breaks down with a combined AI-Human mode (player moves to the newly created team number 5 after Fletcher's betrayal).

FA Mission 6 (Overlord) with Combined human-AI armies. https://pastebin.com/yAmjETHf

Could you add support for foreign engineering units (units sharing)? Now, as far as I understand, buildings and experimental units are built сonsidering of GetFactionIndex