Why not get regular or low hex-heads, and counter sink those? As long as there is some chamfer in the bore to prevent stress risers, I would think it should be ok to bore leaving only 1/4" or so. And there are many other fastener options. Button heads come to mind. Shallow bore and you again have at or near zero above the surface. Torque is again limited, but you eliminate the taper issues. Are the bolts the sole locating structure, or can you add a pin to handle locations and load. Bolts are best if used only to clamp, pins (keys, etc) should be providing solid location across the shear.
But confidence? Can't offer much.
That's why I tend to severely over build everything. It takes a good deal of knowledge AND a good (expensive) software packaged to do a full (and accurate) FEA. And I hate to think about building stuff only to have it fail, so over build I do...