It’s not really inconvenient. It’s more a matter that the default behavior is “wrong” — i.e. launching my program with the debugger is not (necessarily) going to do the same thing as launching my program directly (because the same activity may not get launched.)
So, I’m inclined to say, the default behavior should be changed such that instead of launching the first activity found in the list, the front end should determine which activity to launch by examining the AndroidManifest.xml file.
However, that said, I can perhaps see some benefit in being able to direct the debugger to launch a specific activity, rather than the default startup one. In that case, being able to direct the debugger (in any way — UI, editing a file, whatever) is desirable.
You guys have a quality product, I’ll leave it to you what you think you should do. But I do think the current behavior needs at least a warning or something if the debugger decides to launch a different activity than the one bound to the LAUNCHER and MAIN commands. I don’t think the average user will expect that behavior.