OK, maybe we can work something out. You say that no matter which method you use (plain text command line or the Launcher) the application cannot recognize anything. The way the Launcher works, it is changing the command line file, and when FS2_Open runs, it takes parameters from that file. Each time the Launcher opens, it takes parameters from that file and checks the available boxes.
So, when you say FS2_Open doesn't recognize due to Launcher fault, some parameters, let's try to rule out any other possibilities first.
So, the first obvious question that comes to mind wether the FS2_Open changes the command line by itself to a default sate when it opens, or wether it doesn't take the command line file into consideration at all!
So, I would like you to perform this test:
1) Open the command line file, which is "cmdline_fso.cfg" inside your FS2_Open folder inside your user's library, and change it to something else. Write a custom command line with options you would like to use.
2) Save it. (DO NOT FORGET THIS STEP. Many power users seem to forget this simple one)
3) Close it. (do not leave it open)
3) Run FS2_Open.
4) Quit FS2_Open
5) Reopen the cfg file.
Does it contain the same contents?
You can perform the same test with the Launcher if you want. Open the Launcher, make changes, close the Launcher, (do not start up FS2_Open, you don't have to), and then reopen the CFG file. Do you see the command line arguments you checked in there?
If you do, then it's not a problem of the Launcher, it's a problem of FS2_Open. If FS2_Open sees a parameter in the command line file that it doesn't recognize, it will display an error dialog. If it recognizes a command but doesn't do anything about it, maybe the feature is obsolete, and maybe things for FS2_Open have changed and while I was studying for my exams and I didn't notice!
EDIT: I forgot to mention that the Launcher saves the user's options, each time before it Launches FS2_Open, and each time before it closes. So no matter if you press the save button or not, things should work. The save button exists in case you want to perform changes into many standalone mods. That way you can save your changes without having to run or close the app before you select the next available standalone mod.