Hey Scott,
sorry for my delay on your post. have been busy within the last weeks ketching a deadline.
encore could easily handle compressor-encoded AC3. it wont be transcoded if you´ve choosen AC3 instead of WAV in encore-transcoding/project-settings. you could do only neither nor – not both at the same time.
by the way, if you would like to create AC3 for BD, you can create a generic AC3 with 640kbit/s – this will work also.
encore is low end (and buggy) – even apple DVD SP have been better – you could do scripting and a lot other stuff, as mostly requied.
toast is a consumer-product, which has no professional authoring-capabilities. but it´s a required tool in all authors toolset.
danny