When using Surface image stabilization, Autostakkert appears to run the Surface Stabilization and Buffering and Analysis steps twice. First, when you Analyze, which you are forced to do before you can place alignment points, and again once you click Stack.
Is it really doing those steps twice? If so that might be a legitimate reason to pre-process in PIPP. SS and B&A take 56 minutes on one of my 120 GB lunar SERs, on my 32 core workstation with 256 GB of RAM. If it's doing it twice, which it certainly appears to be, that's kind of absurd.