In the end of the episode when the Docter walks out of the holodeck, he isn't wearing his
mobile emitter, but is able to walk out and onto the rest of the ship.
The Doctor's program has the ability to expand with new subsystems.
Why not simply add the exobiology programs to his own matrix, instead of going through the motions of creating a consultant?
In "Message In A Bottle" Harry Kim struggled with the task of creating
a holographic doctor. The episode implies he spent several hours designing the holographic matrix and assembling the appropriate medical knowledge. And to
top it off, the thing fizzled out of existence because it was too complicated a program. Here, less than a year later, Harry is able to create a perfect
holographic doctor in a few mintues with some simple voice commands.