Fixes#2650.
We have historically relied on merging inputs and outputs in several places in the engine. This used to be necessary, as discussed in #2650 (comment), but our core engine model has moved away from depending on this. However, we still have a couple places we do this merge, and those places have triggered several severe issues recently in subtle cases.
We believe that this merging should no longer be needed for a correct interpretation of the current engine model, and indeed that doing the merge actively violates the contract with providers. In this PR we remove the remaining places where this input + output merge was being done. In all three cases, we use just the Outputs, which for most providers will already include the same values as the inputs - but correctly as determined by the provider itself.