Turns out this was just a language/miscommunication error.
6. Running/debugging the application on the device:
6.a. Build/Debug directly on device
- edit 'Run.bat' and change the run target 'goto desktop' by 'goto android-debug'
- build & run as usual (Ctrl+Enter or F5) to package, install & run the application on your device
6.b. Debug occasionally on device
- Debug-build from FlashDevelop (F8)
- run 'PackageApp.bat' to package and install a debug version of the application
- start FlashDevelop debugger: Debug > Start Remote Session
- start the application on device
- the application should connect to FlashDevelop interactive debugger as usual
As the compiler in my head was parsing this, I read "6.a Build directly on the device." Nope, I don't want to build ON the device, I want to build ON my desktop and push it to my device!
So I skipped ahead to 6.B and started using that instead. I didn't understand that the "... and Install it on your device" line was intended for *me* to do, and it wouldn't happen automatically.
Turns out "run.bat" was all I ever needed
Maybe a quick language change in the text file will avoid confusion for others? Or maybe I'm a beautiful and unique dummy.