1. Is it possible to have my Apollo BTC change it's mining configuration from ECO to Balanced and/or Turbo Mode at night each night without any input from me? I'm thinking a kind of chron job/automation given this is a Linux box.
Yes, I did that. I configured Apollo so it's turned off/eco mode/balanced mode, depending on temperature read from external source.
You can easily program different speeds by time schedule, by using Standard Apollo via USB, connected to any controller like Raspberry Pi. In Pi, make a script for killing apollo-miner process and launching apollo-miner in desired mode again. Finally, add scripts to crontab, so they launch when you need them.
Scripting Apollo speed according to external temperature sensor is more tricky but it serve me very well.