@ITwrx
I've fiddled around a bit with your script and another one by myself and found a few things:

aa-exec /path/to/script.sh or exec /path/to/script.sh will only work (reliable) from the terminal app, at first it wouldn't work via adb. Just tested it again while writing this lines and now it works via adb shell as well 😜 however, exec will close the shell when your script is executed, aa-exec or bash your_script.sh will not. (This is just FYI, not related to your goal) If you include the line X-Ubuntu-Application-ID=my_script you can execute it via adb/terminal app using ubuntu-app-launch my_script and this has interestingly different errors when run from adb (WARNING **: Unable to find keyfile for application 'my_script') and terminal-app (WARNING **: Unable to start app 'my_script': Keyfile does not represent application type) respectively. I think this is the actual problem which is somehow related to the Glib key-value file parser. (the type=Application value in the desktop file AFAIK) i think it is somehow related to the Ubuntu-App-Launcher however with my skills this is as far as i can get.... After running the command ubuntu-app-launch my_script a second time (there is some magic going on that makes doing the exact same stuff multiple times have multiple results ;-D) the error changes both via adb and terminal to ** (process:16881): CRITICAL **: Error parsing manifest for package 'my': my does not exist in any database for user phablet ** (process:16881): WARNING **: Unable to start app 'my_script': AppID is empty

I hope this may help you or others, if you find a solution how to make the app-launcher believe there is a correct keyfile or whatever the problem here is please let us know!

Addendum

I just wanted to say that either something with your script or with my phone (Nexus 4 on old Multirom Ubuntu Canoncial 15.04 r602) is strange. I tested with another script i called "skript" that had a similar .desktop file, only with the X-Ubuntu-Application-ID=skript and this always puts out the same error when trying to execute via ubuntu-app-launch skript (WARNING **: Unable to start app 'skript': Keyfile does not represent application type) but for your "my_script" that i placed in the exact same places as you described, the beahviour was on first try the same, then it changed to the error above which seems to indicate that the ubuntu-app-launcher doesn't get the "_" and than thinks the AppID (which is declared in the exact same way as for my skript.sh) is empty.... and if i change the X-Ubuntu-Application-ID=my_script to X-Ubuntu-Application-ID=myscript the "parsing manifest for package 'my'" error vanishes but it still thinks the AppID is empty

(by the way, skript.sh is just:

#!/bin/bash echo "simple test echo"

and the .desktop file

[Desktop Entry] Version=1.0 Name=Skript Exec=exec /bin/bash home/phablet/Documents/skript.sh Icon=home/phablet/Pictures/carrot.png Terminal=true Type=Application X-Ubuntu-Touch=true X-Ubuntu-Default-Department-ID=accesories X-Ubuntu-Application-ID=skript

)