In this case the referent is the idea expressed as an infinitive phrase (clause?): "It makes sense." -> "What?" -> "To have the security manager be a Java application so that you didn't have to port to all the different [platforms]."
Oh, yes, sorry. Still, the same goes for
to-infinitive clauses. Look at the following sentences:
It's hard to fall asleep.
To fall asleep is hard.
It's a good idea that you leave now.
That you leave now is a good idea.
I wish I knew how to explain the grammar of the first sentences of each pair ('extraposed' subjects or something like that?). I believe that the
its are best regarded as dummies, but you can understand them as anteceding the longer subject phrases. In that sense, they're clearly anaphoric. You can't use
this/that with this kind of reference.
(It looks like it's just you and me again, Alexey. How did that happen!)