Yes. Baton fully decodes and analyzes Dolby-E audio.
Baton can analyze all the common audio parameters: Bit rate, number of channels, sampling frequency etc, audio qualities issues: Loudness, Silence, Noise; and other Dolby-E specific parameters like Program Configuration, Guardband etc.
For a complete list of checks, please refer to Baton Testplans. Baton testplans can be accessed in the Baton UI from Planner -> Testplans.