Could someone explain the benefits of this pose in comparison to just a regular routine of sit ups? How is breathing while holding this pose developing my abdominal muscles? I like to think about all the little changes going on inside my body while holding a pose and breathing.

The main difference is that boat pose is a isometric engagement of the abs, vs. an isotonic sit up exercise. Slow deep breathing in boat pose will strengthen the diaphragm.

Thank you for explaining what is going on inside. Can you list a few more abdominal poses for me to research? Or other standing or seated poses? I am practicing at home and have several websites I read to teach me how to do the pose, including the very good sequence builder on this website. I am interested in the abdominal region because I have heard that some ancient healing traditions focused on the torso as the source of healing. I live in a very polluted city right now and when I come inside from walking in the smog I want to have a few poses I can do to work on chasing all the pollutants I have inhaled back out of my body, or converting them into good energy in my body. Currently I like tree pose, upward facing dog, frog, and boat pose. If I should continue working on these first, that is an acceptable reply, but since I don't have a current teacher, please advise.

There are not a lot of poses that specifically target the abdominals, but we have a list at: http://www.yogabasics.com/core-strengthening-poses.html
You might also want to try and incorporate some Uddiyana Bandha into the poses you are practicing: http://www.yogabasics.com/learn/uddiyana-bandha-the-abdominal-lock.html
And also use Kapalabhati Pranayama to help purify and strengthen the abs: http://www.yogabasics.com/practice/kapalabhati-pranayama.html