Automatic Music Transcription (AMT) relies on paired audio--MIDI datasets, implicitly assuming near-perfect temporal alignment. However, widely used piano datasets have been shown to contain alignment errors that may bias model evaluation and training. We propose a framework for evaluating audio--MIDI alignment scoring methods through controlled temporal, pitch, and structural MIDI corruptions. We also introduce STI, a scoring method built on AMT models, and benchmark it against existing alignment scoring approaches. Our results show that STI, together with methods based on CENS and spectrograms, achieves the strongest overall performance, with STI exhibiting the highest sensitivity to fine-grained temporal misalignments, the main alignment error in AMT datasets. We then apply the best-performing methods to widely used piano AMT datasets and identify trends in their relative alignment quality. These results support more informed dataset curation, model training, and AMT evaluation.

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