In industry, you never have a pin and a hole made of the same material. If they jam, they will basically weld themselves together. One is usually a milder or softer material meant to be replaced with wear.
In particular is the Diaclone Pilots. They have metal pins for the which the arms/legs to hitch onto. It lessens the wear. I was considering only making half the mold and then putting in the pin by hand and then pouring the second half and thought that left too much room for error. Plus I want the resin to 100% cure around the pins I make for this.
If it doesn't work, I can simply remove the magnets and fill in the space with more silicone.
Now to wash it up and pour the silicone and see if it works. On a personal note...I always make one alignment peg different than the others. Its easy to get confused when pouring and get your orientation of the mold halves mixed up.