Does the onboard flash really bother anyone?
It does bother me. In fact the pop-up flash in the D810 is partly responsible for skin damage occurring when using the shift lock of the PC-E 24. Last week due to frost bite, and back many years ago with the D700 the skin wore off my fingers trying to use the lock. The issue is that the pop-up flash housing doesn't allow the shift translator knob to be on that side of the camera (no problem on D3X for example, or other pop-up free Nikons), so for shifts along the long axis of the frame, the translator knob has to go on the opposite side (camera base) and the shift lock knob is under the flash housing overhang (with D3X it is in front of it). Both knobs are easy to access with the pop-up free cameras but a pain to use on pop-up "featuring" cameras. Last week accessing the knob forced me to take off my gloves (in -25 to -19 C, 100% RH, 8m/s wind) leading to a host of painful red spots on my right hand. If the D810 (which is the best camera to use with the 24 PC-E because of its image quality, if it were not for mechanical problems) didn't have the pop-up flash, my hands would be in better shape. Also when using the lens on D3X, it can be taken off in almost any orientation, and then, depending on the orientation it was in, it can't be mounted on a camera with pop-up intrusion, without rotating it back to a specific orientation where it can be mounted on the D810, and the only easy way to do this rotation is to mount it back on the D3X and figure out what the correct exit strategy is, that allows it to be mounted on pop-up flash cameras. One could argue that it's a design problem of the lens, or the cameras, either way, it is a pain for me to use the lens with the D810 (or D800, or D700).
Also it is my experience that using the pop-up as a commander is a big hassle and practically never results in acceptable photographs. There is leakage of light (even when turning it to commander only, the sync flash pollutes the foreground of the scene), there is almost 100% eye blinks or squints in at least some of the subjects (this can apparently be avoided by adding a strange add on device to the flash), and the recycle time is almost eternity when trying to catch good expressions in a group shot, basically after a few flashes quickly, it seems like the flash needs to cool down for 20 seconds before it lets the camera fire again. None of these problems exist with the SU-800. To me the pop-up flash is a feature that interferes with the way I work and I'm willing to pay significant extra money for a camera body just so that it doesn't have the pop-up.