maybe you could, there are certain chords that go super fucked up when played in certain intonations, if you wanna get freaky about it tune every single chord and track that, it's gonna be a pain but it can certainly give nice (or at leaste interesting) results, i found myself in the very same situation before, having perfectly calibrated guitars, not-so-new strings (but new enough), and all pickups in place... but sounded out of tune... it's just the very nature of the guitar. Tune with a real tuner and do it in every single chord = tightness. (and = pain)