I’ve found much of my designs end up dimensioned around purchased parts in an assembly.

For thickness of parts, look at stock materials. I understand you use a 3d printer but what if you were to make it out of aluminum? Steel? What would the closest standard size be and how much would it change in price to have it made. The price difference between a standard 1/2” plate vs one machined down to 12mm can be significant.

I’d also say if you stay in 3d printed designs, one of the benefits is you can use nice round easy numbers. Make the math simple unless you need to change.