If you use a router table, it shouldn't matter that the bit has a guide bearing, as it will be below the table's surface where your workpiece never contacts it. You set the amount of chamfer you want by bit height and fence position, then just run the board along the fence. I recommend a trial pass or two with scrap first.
And yes, do the end grain first since it's prone to chipout at the end of the pass, and that will get cleaned up when you run the non-endgrain sides (though if it's a true butcher block, the end grain is on the top and bottom of the board, not at its ends, so order of cut isn't as much of a factor).