OK; think I understand.
In Finale, you set up the full score with all transposed instruments, as they will appear in the final (published?) full score, and as they will appear in the parts. But then, if desired, in the Document Menu there is an option to "Display in concert pitch". Does Sibelius not work in a similar way?
As regards the question as to the bass clef bass trombone, The answer is rooted in the historical background of the early brass bands. The reason that all the instruments were written for as transposing instruments was so that players could move between instruments as necessary (dictated by the availability of personnel) without having to re-learn different fingering systems. IOW for example, a cornet player could move to Eb bass, and once his embouchure had adjusted to the different mouthpiece, and his ears had adjusted to the change in pitch, a written 'C' scale was still read and played with the same fingering. This system could even be applied to treble clef transposing trombones by equating open to 1st position, 2nd valve to 2nd position, 1st valve to 3rd position, 1+2 to 4th and so on down the chromatic scale. The reason the bass trombone was excluded was because in the early days of the brass band movement the instrument was pitched in 'G', therefore there was no correlation between the slide positions and those of the Bb trombone or the other valve fingering system, so it was assumed that once a bass trombone player had learnt to read and play, there was no real prospect of him switching instruments without having to re-learn a different system, therefore it was left in bass clef concert pitch. If you go back far enough, you will even find brass band scores with tenor trombones written in concert pitch tenor clef, for the same reason, although of course it is less difficult to cross between concert tenor and Bb transposing treble, because of the notes being on the same position in the stave.
Lecture over; sorry!