Pilot Training

Both the profiles that you have mentioned here are way different from each other. There is nothing comparable between them. Hence, there are only and only difference.
Commercial Pilot flies the plane and does the operational duty for the airline whereas someone who has done B.Sc. Aviation might be working for any department as per the company requirements. It may be operations, ground handling, ramp duties, cargo, hub control, etc.
B.Sc Aviation is merely a graduation degree which allows you to call yourself a graduate and hence, eligible for any job that requires it's candidates to be a graduate.
And, on the other hand, Commercial Pilot Course is a professional training which helps you earn a Commercial Pilot License and hence, you qualify to apply as a pilot for any airline that is hiring fresh CPL pilots.
I hope the things are clear now!

In a year, based on recent statistics, approximately 26 lakh graduates pass out of the Indian Education system. Can you guess how many of them ended up with a job (A job commensurate to their education) on completion of their graduation? 30%? 20%? Nope. An appalling 8%.
Of the 15000 odd CPL holders in India, roughly about 5000 are working in the airlines. So, you do the math and figure out, if it is as tough as otherwise to get a job.
Leaving the stat aside, how tough or how easy it is to make it big in any career, depends predominantly on your caliber and the quantum of effort that you put in to equip yourself to be among the best. I have come across tons of CPL holders who whinge about the competition in the job market in India. To them, I state one simple stat. In any recruitment drive conducted by a major airline in India, roughly 4000 odd CPL holders compete for 100 spots (which has been the case for the past 5-6 years), which means roughly 1 out of every 40 get a job. And, there are six major airlines, some of which conduct such recruitment drives all the year around. When you graduate with a degree from a college, you are looking at a competition of 1 in 10000 to land yourself a decent job. So, decide for yourself as to where the competition is at it's toughest. If you don't have it in you to be the best one among 40 candidates, then it is a tough luck. If you have it in you, then you are looking at an illustrious career, with everything being fed to you on a silver plate all through your life.
Yet again, people keep complaining, that only if you have a jack, you would be able to get into the major airlines, i.e complete BS. I have seen a lot of my friends get in simply without that, simply because they persevered. I myself had none, yet have worked with two of India's major carriers. It is sure, that jack works in aviation (where the hell doesn't it , in India), but that's not everything. You can be your own jack to get into an airline.