I didn't read the article until just now. :-) As we all know, Amiga computers have a lot of special purpose harware that does things the CPU just can't do on its own.
Fast forward to present day, and we have special purpose hardware for just about everything but decoding of audio data. Yes, you get DMA to/from the sound card, but the CPU still has to put the data in a format recognized by the hardware. While decoding the data, the CPU also has to do all the other stuff its supposed to do, so you end up starving the audio interface of data, hence the skips.
Sound cards have DSPs, so you'd think it would be possible to write a decoder in the DSP itself and pump the data via DMA. I really don't know enough about audio hardware and various operating systems' audio subsystems to say.
In any case, there are always trade-offs when it comes to task scheduling. In the case of AmigaOS, which is effectively landlocked in single CPU land, the trade-offs are pretty much the same as they were in 1985.
I haven't read the Anubis stuff yet, but if they're planning on effective memory protection and multiple CPU support--one would assume so, using the Linux kernel as a base--it should be pretty cool.