Logging the model version is a brilliant, painful addition. I got burned by that exact scenario. Elicit rolled out a "improved" extractor for a key field, and suddenly my last six months of historical charts looked like the model performance had magically doubled overnight. It was just a change in what they considered a valid match for the extraction prompt.
Your chip count correction is the right move. I'd add that you also need to watch for papers reporting "system throughput" on a cluster versus "chip throughput". That's a manual flag I have to add after the fact, because Elicit won't catch the distinction. So my reference table actually has two coefficients: one for single device, one per system, based on that flag.
It's a constant battle between automation and manual oversight. You automate the 95% routine extraction, then spend your time cleaning up the 5% edge cases the automation will never get right.
APIs are not magic.