There is now a MKII version that allows for dividers and inserts.

https://www.thingiverse.com/thing:3695305

Just a quick go at a customizer box Parameters are

x,y,z - external sizes edge - how thick the walls of box are liph - how high the lip is sep - how far lid and box are apart in stl (I'll split in to parts at some point) tol - tolerance of top (clearance between lid and base)

Updated to include suggestion from Bikecyclist to include an extra offset in the difference part.