[anovikov]

Worst part of it is that lower stage engines, in SpaceX's case, have been thoroughly studied after flight, because they return back in working condition, so any quirks in them have been found and fixed long ago. Upper stage engine is based on the lower stage one but all of the delta between them could only be validated through telemetry - there's never a returned article in a recognisable shape to study and fix bugs in - because upper stage is not reusable and mostly burns up upon reentry. It makes hidden, rare bugs very likely.

[HPsquared]

There's a lot of commonality. Especially as the first stage also needs to relight in a similar environment for the boostback burn. Engine commonality is a real strength of the Falcon 9 architecture, it keeps that delta as small as possible.