I would not sweat it to much. I suspect that once you mock up your plumbing, you are going to find that the box will need to come past the edge of the bracing. The box needs to be wide enough to get the elbows in and out, (threaded ells/street ells preferred) and you need to be able to get your hand inside the box.
No need to get fancy, I would suggest a full length L shelf, put in in two pieces. You have ~ 2.5' clear and ~2.5' partially hindered, piece of cake. Dry practice, till you come up with a solution. Silicone goes on the piece of glass being put in place, but in the end that does not matter so much for an overflow box.