You can do this by hacking an XML file. There is a tag that can be added after the clef definition.
Examples:
For an instrument in D
<clef number="1">
<sign>G</sign>
<line>2</line>
</clef>
<transpose>
<diatonic>1</diatonic>
<chromatic>2</chromatic>
</transpose>
For an instrument in B♭
<clef number="1">
<sign>G</sign>
<line>2</line>
</clef>
<transpose>
<diatonic>-1</diatonic>
<chromatic>-2</chromatic>
</transpose>