Butt joint is preferred over lap due to the fact that a butt joint will not trap moisture. If welded correctly the weld should be stronger than the surrounding metal. Also if you have a lap joint then one piece of metal is displaced more than the other resulting in more filler to be added. The more filler you use the worse off you are. Fillers are to be used to fill imperfections and to smooth out not to build up a large area. No filler should be over an 1/8" thick at the most. I've worked on fenders in the past that look great until you grind a little and find over an inch of filler. I've seen front fenders with more money in cheap bondo than a replacement fender would have cost. Use the least amount as possible.
I think that depends on the material being welded. Thicker material, where you can get good penetration withoug large gaps in the metals, the butt joint is strong. For body work, where the metal is too thin to bevel to get penetration without burning through or having to grind off the weld it is a different story. ICAR, the organization that sets the standards for Auto Body Repair, recommends a "backer" behind any butt joint. They recommend either a lap joint or butt joint with a "backer" that is plug welded on place for any patches. A lap joint done properly should not need an axcessive amount of "bondo" to complete the job, and will be stronger.
My personal rule of thumb is lap joint if I can get to both sides to seal the joint. I always use weld thru primer on the lap joints to help resist corosion. I also use a crimper to make the two finish surfaces even. On butt joints, I will clamp in a backer when possible and I also start with about 1/16" space between the two surfaces to help reduce distortion and creep.
I prefer butt for exterior body to eliminate moisture trap and for cosmetic appeal- thinner on both sides-, lap for inner fenders, floorpans, etc. for strength- when you use a flanger the two pieces are level and it takes very little fill. Eastwood has a hand flanger but J.C. Whitney and Harbor Frieght have pneumatic ones for little cash- makes it quick and simple to make a 'step' flange on back metal piece.