I am thinking about using a Raspberry Pi 3b using dietpi and 3 docker-OptoPrints ti control my 3 ender printers. Does anyone see anything wrong with this setup, before I go an spend all the time setting this up?

Should be fine, what are you going to use to get the data from the RPi to the Printers?

You might also look into getting USB Ground isolators just in case the power supplies have different grounds, which could cause issues with the signals