I am not familiar with the terms C.O. and Certs, they aren't used in the states where I practice. An agent from New York will likely have to weigh in on that.
At the end of the day purchasing a home from an owner vs. purchasing a home from the bank will have the same net result. The buyer will own the house. The process will be a bit different and in some cases there are some fees (as you have mentioned) that the bank mandates that a buyer pay that may or may not be paid by the seller.
Practically speaking the transactions are very different however. A seller has needs and wants as well as emotions. For the most part banks have formulas and either you fit the mold for them or not. While it has gotten better with the recent foreclosure issues banks are facing, the general rule has been that banks don't normally have a time frame. I have worked on bank transactions where it has taken over a month to get an answer.
Consider a bank owned transaction carefully. You may get a good deal but you won't walk away feeling warm and fuzzy. You will either do it on the banks terms or not at all. They will win nearly every disagreement, and you will be left feeling like you gave everything and got nothing. In the end however, there are some great deals to be had when buying a property owned by a bank. I hope that helps.