Mike fixed the prescaler bug in V2.12.28, I was using an older version which was definitely not right.(CSpect DMA prescaler works for me in V2.12.29 correctly ... I wasn't aware of V2.12.30 .. time to re-test it and refresh the "known bugs" page on wiki, hm)
As for the copper, it's a shame there isn't a means to set C-PC directly, although using FRAME mode and a pair of interrupts per frame at lines 64 and 192 to refresh the copper list in two halves works well enough for my purposes. However, now I've got DMA based audio working as well, I'm tempted to just use that instead as it removes the dependency on interrupts and leaves the copper free for visual effects.