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You conclusion is correct " that the model is using the EIRFT curve to get both the "EIR-function of temperatures" and "EIR-function of PLR" modifiers." A new issue has been posted to fix this and there is some additional explanation there. See #7590.
Because the same curve is being evaluated (incorrectly) with the temperature variables first, and then with the plr, the output reporting for that curve will hold the inputs/results of the second invalid call.
Regarding the transition for Table:TwoIndependentValues, another user just posted an issue noting the same problem. See #7588.