@linuxgurugamer
Returning to KSP after several years, and for the first time playing with the DLC, I have discovered that Engine Plates and SmartStage do not want to play nice. Specifically, SmartStage will lump all Engine Plates (and their associated engines) into one stage, and for good measure include the next decoupler up as well. Ironically, the stock Reset button will, at least for the craft I used for testing, produce staging that is less wrong and easier to sort out manually.
Replacing Engine Plates with decouplers fixes all staging issues on test craft.
Craft file (a stripped-down version of the craft that led to the discovery):
https://pastebin.com/pwGKdLrr
Log file, in two parts:
https://pastebin.com/NingbDVB
https://pastebin.com/nFpVfCUD
Relevant actions performed:
Load craft; use stock Reset; use SmartStage calculation; manually fix staging.