Walls – Re-using Stud hole in wall

I think the answer would really depend on the flexibility of the bar top. You could test the flexion of the board with a jig, and if it's up to muster, then the only other concern is the back corner. That is where the force on the outer corner is going to transfer to, in an upward manner. You mentioned that the angle iron is going into 2"x6"s, so those should be fine.
If the grain of the butcher board runs lengthways, I would stick with the threaded rod, but if it runs the short way, you might run into compression/differential problems with the glue joints.
It's a very smooth idea, I hop you can make it work!

Typically you would remove them, however the anchor you are using is marketed as a "stud solver" meaning that it can be driven into a stud. I think it is fine to leave them.

If you were using small plastic drywall anchors then I'd definitely remove them and drive a screw directly into the stud.