You can do it with staff styles.

Staff styles can be different between score and linked parts.

In the dialog box Manage Parts, create three different parts: Flute, Saxophone, and Clarinet.

Each of the three parts uses the same generic WW staff (in Concert Pitch, I suppose) from the score.

In the Flute part, use the Concert Pitch staff as it is.

In the Saxophone part (but not in the score!), apply a staff style with Eb transposition.

In the Clarinet part, apply a staff style with Bb transposition.