BTO stands for Build to Order, it can also be called CTO or Configure to Order.
Refurbished Mac's enter the refurb program for a variety of reasons, all machines are checked and re-checked. Those reasons can include being returned because a wife got angry her husband spent some money, a warranty issue or new models were introduced. If the machine fails the checks for any reason it's fixed and retested before being sold. They also have the same warranty as a new machine and are also eligible for AppleCare, this means Apple stands behind them the same as a new machine.
In the extremely rare event there is a problem if it's discovered within the first 14 days of ownership Apple will refund or swap out the machine, it's your choice. Apple Stores do not sell refurbished machines so they do not have the authority to swap or refund you need to deal with the online store. However if the machine does need service after the first 14 days you can take it to any Apple Store or AASP (Apple Authorized Service Provider) and they will repair the machine.
Most people that buy Apple refurbished products are extremely happy and cannot tell the difference between a new machine and a refurb other than the box it's delivered in which is plain, no graphics on the exterior.
I would recommend investing AppleCare which will extend the warranty to 3 years and include telephone support too. You can buy this directly from Apple or you can save by buying from resellers such as Amazon or LA Computer Company.
Enjoy your new machine, I'm sure you will be extremely impressed.
BTW it sounds ilk you are switcher from MS Windows if so then I'd recommend bookmarking and using:
http://www.apple.com/support/switch101/
http://www.apple.com/support/mac101/
http://support.apple.com/videos/#macosx106