I think it's a really, really bad thing that the breakout boards for Arduino don't follow any noticable standards. IMO, the hole configuration should follow a strict standard. Then, Arduino cases for example could be made to host one or more breakout board easily and safely fastened inside the box. No matter if it's a real time clock, a relay, or any other kind of module.
And, better yet, using a grid of multiples of 8mm c/c, holders with LEGO stud compatible interface could be 3D printed to hold the breakout boards to a LEGO baseplate instead of swinging around randomly and threatening to short against the nearest next board.
Yes, as you can see I'm an Arduino fan, so I'm thinking inside the Arduino box. But I see no reason this shouldn't apply to most systems.