Having multiple wakelocks doesn't affect the battery consumption (if they overlap in time). As long as there is at least one wake lock the device will not go to sleep, so having a second wakelock does nothing.

In reality (at least in BeyondPod's case) there is only one wake lock, I think the issue is how Android battery statistics code counts wakelocks when 2 process are involved in the same playback (the application process and the Media Server process).

I did several experiments using Google Play Music as a baseline. In all experiments I charged the device (Stock Galaxy Nexus 4.1.2) to 100%, rebooted (to clear all old battery statistics) and did 1 hour of audio playback with max volume over the speaker.

Here are the results as displayed in the standard Android battery usage screen:

Gogole Music: MediaSever 35%, GooglePlay 25%.
BeyondPod: MediaServer 33%, BeyondPod 28%

If you tap on each process it will tell you how long did it keep the device awake - for Google Play the awake time was a split 32min Media Server, 28min Google Play (both together account for the 60 minutes of playback) BeyondPod's times were similarly split.

In both cases the device battery went down by 4% - from 100% to 96%.

The results may be device specific, but based on the above data, I don't think there is a significant difference between the way BeyondPod is using battery when playing (at least compared to Google Play Music).