It might be the state undo logic slowing down blockchain processing in a sequential manner (this computation is probably skipped for replay+validate). But I doubt there is a way to disable it to check that, short of modifying the code for the test.

Probably we should modify the code dealing with checkpoints to skip undo logic up to the checkpoint. This would allow us to confirm if it is the bottleneck, and it would also give us a speedup when checkpoints are set if it turns out to be the bottleneck.