When playing original keyboard compositions by Bach (not transcriptions, where pedaling would depend on the arranger’s intentions) I sometimes use the damper pedal to bring out implied harmony when counterpoint isn’t in progress. The pedal can help to amplify a single chord, like a final one of a movement, for a more effective ending. It can also help bring a new texture to a pattern or passage built on a broken chord. For example, the beginning arpeggios of the Fantasia in C minor, BWV 906 provide a justifiable pedaling opportunity since all of the notes outline one chord so their function is clearly harmonic. By the same token, in a piece like the famous Prelude in C major from WTK II, every separate harmony could be pedaled, carefully. I am sure Bach would experiment in that direction, had he the opportunity.