COuntersink the hole. If you look at commercial amps, you often see the bolt hole has an indentation in the bottom panel to clear the bolt head. And they use a carriage bolt - the bolt with the smooth slightly rounded head. But certainly a flat head bolt would work for limited clearance. You might countersink the hole for a bit more room.
IMPORTANT: if you run a bolt through the bottom panel of a metal enclosure through the toroid, DO NOT let the bolt be long enough to contact the top panel. If you let the bolt touch both top and bottom panels, it creates a "winding" through the toroid, a winding that is shorted end to end. This will have disastrous effect.