The approach of this tools like Google Blockly, Stencil or any others, is time saving. Simple said: if you're able to connect Stencyl blocks in the right way, you're also able to write code, but you need more time to configure your setup (i.e. frameworks, tools like Levelhelper and so on).
Look, the Google Example for Blockly:

is an good example. In plain text it looks like this:
if get(count) > 256:
do:
set(count) to 0
print "Game Over"
endif
In Java this could look like this:
if (count) > 256 {
count = 0;
System.println("Game Over");
}
Finally, the code generation tools (or rapid prototyper, call it what you want) are more or less tools that use predefined code blocks you can combine and prevent you from making mistakes by offering a fool-proof editor (sorry, Stencelers don't want to offend us!).
Think of a bike with training wheels. But a very powerfull bike. With highspeed training wheels. :-)
And don't mix two different stories:
- Stencyl is for 2D game development.
- The back-end development is something complete different.
If you want to archieve fast results with little learning, try something like
Modelbaker. You design the data model (remember: persistence) and the necessary controllers (the logic) and helps you with the front-end (i.e. views). Those views are the part your game is calling (think of an more clever replacement for the php-file in my example).
Cheers,
Heiko