As mentioned previously, even rerouting software such as Soundflower or Boom will cause the glitch on the internal speakers. Boom has found some way to work around the worst of it (perpetual audio stuttering), but they've been unable to completely get rid of suttering in some system sounds.
In another forum for DPS (another software audio rerouting solution), they say that Apple has not provided any guidance about changes in the way Core Audio functions, so it's hard for developers to fix an issue like that. To quote them:
"It seems Mavericks has issues with any audio kernel extension but there are no errors or documentation yet regarding this or changes to Core Audio for OSX. So we have to wait… We have narrowed down the choppy audio with video issue to Mavericks and QuicktimeX. This issue happens with any audio routing software, not just DPS."
http://dpsinsider.com/forums/topic/mavericks-osx-issue-list/
I have a hard time believing that it's all these developers' and hardware makers' collective faults when Apple's own software are the main culprits.