I think you're over thinking this. I have used boring bars down to .016" min bore with a .009" Ø neck. Other than sweeping the drill pocket to within like.0002" and triple checking the initial touch off, i just set small boring bars like regular, just with more attention to initial precision. The flat tip set screws do a pretty good job of finding center. Make sure you center the flats as much as possible initially. Then tighten the screw, loosen just a tiiiiny bit, wiggle, tighten, loosen, wiggle, tighten. This will get the tool holder centered on the flat pretty darn well.
If you watch the video for the Genswiss system, you will see that it accounts for runout of the guide bushing, so yes, it should give you true center within a couple tenths. (that is a couple ten thousandths of an inch or .005mm - plenty accurate, basically the same as a tool maker scope)
If you dont want to fork out big bucks for the genswiss system, you could use the "face bar, stop spindle, jog off, cutoff, measure nib, offset" method. This is slow-ish and annoying to do each time you replace the tool, but if you're breaking bars consistently its worth it.
If you offset a new tool minus a few thou, measure the first part then offset do you still have problems?
Do you think you are breaking the tool because X is off, Z is off, or you centerline is off (cutting above/below center)?
Also, can you program in some redundancy? If this is a known problem tool, can you lighten the DOC or feed so there is more strength in reserve to account for unexpected machining conditions? If you're right at the edge of stable with a perfect setup small issues become big issues quickly.