Skinny pipe entering toilet siphon flush

The flapper came off on our siphon flush, so I bought a new one. I fitted it but it was leaking badly.

When I looked properly, I noticed the inner pipe delivering the water to the toilet from the cistern was not flush with siphon flush. This means the siphon permanently fills up with water as below;

Is that normal? Should the connection not be on the outside of the cistern?