During a recent game, my opponent dropped his proxy mines, but the template token overlapped a rock. A quick search of the rules and reference book didn't turn up anything expressly forbidding this from happening, but it also didnt say that it could be done, either.
In the end, we just went with it, and continued the game. Granted, my scanning of the rules was fairly quick, but is such a maneuver allowed. Can a mine/connor net/cluster bomb/explody munition token overlap an obstacle?

It can, and nothing happens as a result.

Edit: Nothing different, I mean. The bomb token still does whatever it does, and the obstacle too. It's entirely possible to drop a Prox Mine on a rock and then have a ship hit both the mine and the rock in the same maneuver.

Don't see why not, it can hang off the edge of the mat and the portion that is off the mat is just considered lost surface area for contact with ships.