There's a lot to address here, but I've shipped a car a couple times so I'll do my best to answer your questions. As far as a difference in quality of service between a broker and a transporter, that really depends on the company. some brokers have a good reputation and some do not--the same can be said of transporters. It's a good idea to call them and see what kind of professionalism they convey over the phone before getting an estimate. I've personally stuck with one company over the years, A1 Transporters Inc, because they were really good about answering my initial questions and seem to have offices all over the U.S.
As far as using an enclosed transport carrier, that's really not necessary unless you're shipping an expensive or high-end car. It does cost more and the small bit of extra protection is more for peace of mind than anything (in my opinion, anyway). Regardless of which option you choose, insurance must be included as part of the cost so you'll be protected against damages caused by the shipper anyway.
I don't know that contacting a local affiliate is any cheaper. There's also a bit of danger in taking the cheapest option if it's drastically lower than all the other estimates you receive. That's usually a red flag and signals a company you should probably avoid, or at the very least, inquire as to how their price is so much lower. Hope this helps.