Okay, now things become more clear
. It's always a bit tricky trying to ID specific elements in all this mess, I know.
If you have server.zips that have implemented changes to the GPO.con, then the Editor\GPO.con is entirely irrelevant. That one is exclusively being used by the editor (as are all files inside the "Editor" folder). This is also the reason why most mappers do not ship their final maps with that folder included, as it only takes up space in the archive and is not needed by the common player.
However, you correctly assume that all spawners and gameplay stuff is situated in the Gameplaymodes\xxx\GPO.con. However, it is theoretically possible to launch code from other files in the archive as well, though why any modder would do this is beyond me. If you use a good text editor like Notepad++, you have the option to "Search in Files..." for a specific word/term. I'd suggest extracting the server.zip locally and trying to find the term "wasp_defense" in all files in that folder. If you see it spotting up somewhere outside the GPO.con in the results, you found it.
How this "run-stuff-not-from-GPO.con" works? The engine doesn't actually care in what file you add your code, it only matters that the file is being read and parsed somewhere along the map launch process. E.g. you could create and add a spawner right in the "init.con", as that file always gets loaded by the game.
Alternatively, you can also use the "run/include" commands to point to other files. If you take a look at the init.con, you'll notice that most of the code in there are simple "run" calls that load all the other required files. The file&folder layout in the level archives is just some sort of standard used by DICE, but the engine really doesn't care about it
So it might be that a modder - for whatever reason - decided to not place his alterations in the usual places, but maybe an additional file or in another existing file.
Problem no 2 simply does not make any sense, I really don't know how to assist there. Kubra Dam really is no different from any other vanilla map in terms of editing it, so I'd really suggest you start over from scratch on that one, taking particular care of what you do on every step. Alternatively you can try fiddling with the debugger (bf2_r.exe) to see if that helps figuring out the underlying issue. But the debugger is best used for crash debugging, not these kinds of things...