There is a 3 step way to edit the counter sinks position.
What you do is measure the bolts length then - the shoulder just the very end of it if it's a 50 mm bolt it's 49.5 mm long, write that down. now go do the joint the first component is the bolt put the joint on the end of it, then put the next joint in on the outside of the bolt hole then offset the holes joint position by the measured length of the bolt.
to double check the bolts depth is correct measure from the shoulder of the bolt to the face of the counter sink, If it's 0 it's gold if there is a distances add that to the offset.
Now to edit swipe the timeline back to the countersink hole do a offset face on the counter sink faces this makes it look the same as drilling the countersink deeper, then move the timeline back to the end
measure the distances from the bolt to the faces off the countersink write that down swipe the timeline back to the joint add the measurement to the offset and done.
Same if you added a bigger bolt.
It makes it look like it would with a big countersink cutter, if it needed a flat side then the counter sink well that's far too much work.
And yes this is a full bore work around that is quite ugly.
If you wont a vid let me know otherwise it's all good.
It was just a fun exercise for me.