Hello,
I just wanted to confirm that your conclusions are correct: OTP2 uses the same street network representation as OTP1, but the scheduled transit network representation (and the router that uses it) have been changed. In OTP1 both the street and transit networks use a graph representation materialized as an object graph in memory: each street intersection, as well as various states of being on transit are represented as node objects connected together with edge objects.
In OTP2 this is still the case for the streets, but the transit data is stored in a much more compact tabular format appropriate for the Raptor algorithm. This is reusing some table data structures that already existed in OTP1 but were attached to graph nodes and edges. Now those tables are used directly, viewed through an interface that is appropriate for Raptor. You should no longer see any of the on-board-transit edges in graphs produced by OTP2.
The literature on the Raptor algorithm makes some strong statements about it not being a graph algorithm - this is true in the sense that it does not operate on a materialized object graph. But it's reasonable to say it's still a graph algorithm (different than Dijkstra's), it's just using a very compact and cache-efficient graph representation that is made possible by the fact that each transit stop on a route has at most one incoming edge and one outgoing edge to the previous and next stops on the route, so memory address adjacency can be used to imply graph adjacency.
Hope this helps,