S.B.
As an HR Manager, 10 weeks is entirely too long for the hiring process. I would bet a dollar they hired someone else and 1. they either quit or 2 got fired. So why if you didn't make it the first time, what changed? Big red flag! Yes, you would burn a bridge with me and you would NOT be considered for another position in our company.
Quality of life is very important. I commute about the same an hour to hour and one half. Each way every day. Train is not an option for me because I live in Houston. $5K more? For that commute? NO WAY. Again, think of quality of life. I would take less to work closer to my home or out of my home.
If it were me, I would stay with Company B. I would tell Company A, "thank you so much for the offer; however, I received and accepted another offer:. You don't owe them anything more than that.