I have built a few racks where the top levels are built to different heights to allow for shoe boxes. This is pretty easy to do.
I have also built several "sideways" racks where each level can hold one 28 qt. box or two 12 qt. boxes. This is pretty normal and I assume is not what you're looking for.
But what I also did was build a series of shims for each level that allowed me to hold four shoeboxes for hathclings. I just had the set the shim on and shelf and the shoeboxes fit perfectly.
A more modern incarnation of this idea would be to build a rack like TWH's where each level can hold one of the following...
One Sterilte 41 qt. box
Two Sterilite 28 qt. boxes
Three Sterilite 12 qt. boxes.
These boxes are very close in height but not perfect. I just measured them last night. You'll probably need to shim the two smaller boxes up with 1/8" Sintra or shower board.
Then you can build another set of shims from something thicker for hatchling boxes.
I'm sure some combination of the above ideas will give you what you want. Depends on the species you keep, of course. I can't recall if you mentioned that.
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Current snakes:
0.2 Gonyosoma oxycephala - (Silver/Yellow)
3.3 Gonyosoma oxycephala - (Green)
2.1 Gonyosoma janseni - (Black)
3.3 Gonyosoma janseni - (Black & Tan)