I finished this bike box yesterday. Cut it out on the laser, glued it with leather glue, and assembled it. I ended up manually measuring where the holes go in the bottom, and tie wrapped it to the bicycle shelf.
I also put foam underneath the box (look at the 2nd picture), to use as a shock absorber. Also, after tie wrapping the box down, I put some foam, and then double stick tape to hold a false bottom onto that, for better suspension. You can see the floating wooden piece in the 2nd to last picture.
I used 3mm birch for this entire project.
I've never made a box like this, but I rode my bike today, and it worked well. It did shake quite a bit when I went over rough ground, but it stayed closed, and my tools inside were fine.

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