Wasn't some parts of AGA fabbed by HP? Presumably because CSG couldn't fab what was required.
I think you are right, CSG's fabs just weren't up to the task, Lisa might even have been some standard HP mixed mode ULA (now there's a thought for another thread!;) )...
I also seem to remember Jay Miner expressing surprise in an interview in the early 90s that most of AGA was still fabed on the original process that they used back in the mid 80s...