It's pretty much the process you describe.
Stansted isn't set up for connections.
As you'll have checked in online, you avoid that part of the hassle and that's it.
Immigration is one part of it, but for security, unless an airport can guarantee that all passengers have started their journey in an EU country, they will have to be rescreened. While there are airports that do this (e.g. Amsterdam or Frankfurt for Schengen passengers), it would probably negatively impact on a Low Cost airport like Stansted because it would have to move from fairly simple passenger flows to a more complex and less efficient setup.