I would think that if you're shooting in the 1:1 reproduction range that the built in flash would be of minimal use. Reason being is that the working distance at that reproduction range would mean the lens might cast a shadow on the subject. For macro shooting off camera flash is a big plus. Many people find a ring flash benificial or the expensive Nikon R1. I have successfully used a single SB800 off camera though. Depends on your shooting circumstances and needs.
As to DOF, it's entirely dependent upon aperture and subject distance. To increas DOF with macro imaging there is only two choices; multi-frame focus stacking and plain old cranking down the aperture. Focus stacking is more suited to static subjects, cranking down the aperture is subject to diffraction. Personally I crank down the aperture and accept a small loss in fine detail which I feel is offset by the gain in DOF.