Hi there,
Thanks for posting and sharing your background and questions. Congratulations on a strong GMAT score as well.
As I see it, you have the following strengths working for you:
-great GMAT score
-strong GPA
-additional online business coursework demonstrates you are dedicated to learning and a hard worker
-sounds like good all-around business management experience, with skills developed in analytical thinking, project management, quant skills, etc. Working on 'viability' and business turnaround sounds particularly compelling.
Potential weaknesses/challenges:
-lack of recent community or extracurricular involvements
-non-IIT
-general competitiveness at top schools-- sometimes need a 'wow' factor and/or to make a big impact with your essays/recs/interview to stand out
Unknowns:
-people skills: have you had to manage/lead people or teams in your role/s?
-leadership experiences?? (these can make a difference at top schools; can be professional or outside of work)
-more about your goals... be sure you can explain your short and long term post-MBA goals, and the rationale/motivation behind them (i.e. why are you interested in management consulting? How will you utilize the skills you've already gained in that career, and how will you use what you learn/gain from the MBA?)
School choice: Not sure of your rationale for the schools on your list per se, but I think it's a reasonable list, knowing that Wharton and Kellogg may be a bit of 'stretch' schools but a lot can be impacted by how you put your overall application together, make your case for why this school is right for you and why you need this degree, etc.
Your questions:
1. I have pursued the aforementioned programs pertaining to business management. Will it affect my application in any way?
For your online/certificate programs? Will not affect things generally; and again I would say it's a small plus that you have made the effort to complete this coursework, and if you apply to a school at which you've done online work that can be a small plus/indication that you really like that school's coursework/programs.
2. I am not a first generation entrepreneur. Though I have worked like an entrepreneur ( starting a business unit from scratch, managing entire operations of the unit) i have been an employee in the business. In this case, will my experience be considered an entrepreneurial experience or not? How important or useful is an entrepreneurial experience?
Entrepreneurial experience can be very important or a big plus... and 'entrepreneurial experience' can be defined in many ways. It sounds as though you have the type of experience that b-schools will value, and you'll just explain what you've done and undertaken, what you learned from it, how it impacted your career choices, etc. I would say it's less about a given label, more about the impact it's had on you and impact YOU'VE made through the experiences.
3. With my profile, is it logical to apply to wharton or Stanford?
It won't be easy; but if you are passionate about either you can give it a shot. Keep in mind that Stanford is THE most competitive school out there, and has a much smaller class size than Wharton (and many other top schools), so it makes it that much tougher, statistically, to get in.

Stanford is a big reach for just about everyone, and usually successful applicants REALLY have to stand out in a unique way.
4. I wish to work for a management consultancy, as a person specializing in operations and manufacturing management. Shoudl I apply to colleges which are known for operations management or to those known for general management and strategy? Specifically, Purdue-krannert is highly ranked for operations. But is out of the Top 30 band that I am targetting. Should I apply to Purdue?
It doesn't hurt to look at schools strong in operations given your goals, but also keeping in mind that all top programs will provide a solid foundation in general management and opportunities to study operations. You have MIT, Tepper and Ross on your list, and really Kellogg as well, which are all strong in that area. If Purdue is of interest, or Kelley for example, you could apply to one as a safety school, but only apply if you know you would consider attending (in other words-- ask yourself, if I got in ONLY to Purdue and no where else, would I go there? If the answer is yes, then by all means. If the answer is, hmmm no I would wait and apply next year, or I'd pursue other options, then don't spend the time/effort.)
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https://www.mbamission.com/consult.php. And/or you can always check back in here with q's too. Good luck to you!