I would suggest a programmable relay or plc for this application.
I've used these for a similar application. You can enable the program to run only when the generator is running(however you choose to do this), using temperature controls/alarms(basically the thermostat) to decide which would be able to run,how many and the starting sequence by just controlling the liquid solenoid valve (and hope they don't leak:whistling)
For example, with just using a series of timers, you may enable a compressor to run but, it may be at temperature or at least not in an "alarm" condition and not need to run whereas a "box" whose temperature is up that needs to run is disabled. Once the temperature is out of the alarm range, it can enable another one to run instead of waiting for a timer to time out. You may have a 30 minute run time but the temp is able to be reached in 10 minutes so, you have to wait 20 minutes before another is able to start.
Also, something to consider with freezers, is defrost, door and vent heaters, and condensate line heaters that will need to be allowed to run.
These are very inexpensive, usually have a free software download or can be programmed at the keypad, and are expandable. You can start with the basics and add features as you go without rewiring.