Just to make one thing clear, black smoke is unburned fuel. So more fuel+same boost=smoke+ little more hp, more fuel+more air(boost)=more power+no smoke. A really good tuner increases engine efficiency which is same fuel = more hp (which = better mileage), does make it a bit more difficult to do, but can be done since these engines had no mileage requirements and only emission requirements.
As far as diesels go anyone can increase fuel to get more power, if you increase it a lot you may have to change the turbo to keep up, the VGT turbo in yours is really nice in acting like a multi-size turbo. If you get someone who knows how to tune really well you can get more power without the smoke.