No rule of thumb that I know of.
I don't like it when 3 braces hit at one spot, but it's happened and probably will again. Make sure there is enough of the post left after the mortises, housings, and peg holes are installed to handle any bending forces or other loads on the post, including the contribution of the braces when they are loaded.
If you can't make that determination with certainty and we're talking about a real building, you should have an experienced timber frame designer or timber frame engineer take a look at it. Feel free to PM me if you'd like any recommendations.
As for opposite braces -- the mortices almost always go all the way through in 8" wide posts, and may in a 10" post. That's pretty normal.
Are you asking in regards to a specific circumstance or just in theory? More information would be helpful...
