Having looked at the code, with WB running WFX will disable animations when in the Skype process. However this has been the case since Skype v4 (it is v8 now). Nothing should have changed recently in this regard.
I imagine it would be a newer WB build to address this as Skype has changed drastically since it needed the special handling, but right now I do not have an estimate for when there would be a WB update.