An MSR bottle is probably safer than a bladder for carrying fuel (less messy, too) and while they do take up space even when empty, it's not like you're touring around the world where every cubic inch of storage is critical.
Yeah the bladders do make me a bit nervous. I can't stand carrying those MSR bottles.
My Baja bike is a KTM 505, with a GL bag, so space is very limited. That extra gallon of fuel seems to be the perfect compliment to my 3.4 main tank. I safer solution would be to buy the 6 gallon Acerbis for it, but it puts a lot of weight on the front end. I try to get the bike balanced as possible.
I keep it on the non-exhaust side strapped to the outside of the bag. But it only only has fuel in it for the first 50 miles, only if it is needed on a particular stretch.
