Probably the best and safest method is to look into the foam used for camera bags. That is the most common customisable option I know of that is practical. You'll spend way less time and likely money if you cut foam to fit and pack everything.
Obviously, I'm a fan of 3d printing. Heck I'm beside my printer that is chugging away at a design I made today. However. I think it is a matter of using the right tool at the right time. IMO, big drawer filling organizers are not ideal for printing. I can make wood cardboard or sheet metal boxes much faster and cheaper than printing.
I could see myself designing a quick 2 rail holder with slots for each device to sit within, but that is going to be sloppy and likely wear poorly on the device. Best bet in my opinion is camera bag foam. If it is good enough for a half dozen $1k pro primes in a bag that gets banged around, it will work for some hand helds.