You might not be sure that is how it was done 2200 years ago, but the Ponovicher Rov, as well as the Sifsei Chaim were, and therefore said the pshat and quoted the pshat.
Nice backhanded way of arguing on it, btw.
As for how I know that midrashim predate the gemarra, Midrashim are from tanaiim, The gem area was closed at the end of the amoraim period, generations later. The gemarra even discusses Midrashim and who authored them
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