Why can't we prove decidability of $L= \{ \langle M \rangle : M$ accepts $ \epsilon \}$ with a configurations graph?
$D$ verifies $\langle M \rangle$ is a (deterministic) TM and then builds the configurations graph and checks if the initial configuration of $\epsilon$ is connected to an accept state (there are only finitely many) and returns true if there is and false if there isn't.


The problem here is that, even if you define the TM so that there are only finitely many accepting configurations (e.g. by requiring that the final tape be empty), the configuration graph itself may have infinitely many vertices. This is because the configuration includes the contents of the tape, and the tape contains however many cells the TM has written to, which is in general unbounded.

Every vertex can be identified by a finite string (the configuration description), and each vertex is connected to only a finite number of other vertices (determined by the transition relation), so the graph is locally finite. But the whole graph may still have an infinite number of vertices that are reachable.