It sounds like there could be a few different issues here. Disabling the hiberfil.sys file through the CMD can cause problems with the sleep function, as this file is used for hibernation. If you want to use sleep properly, it's best to leave this file enabled. The hiberfil.sys file is not necessary for the mechanical hard drive to spin down, as this can be controlled separately.
It's also possible that the minimum power state for the CPU cooling is not being controlled properly if the fans are not on the CPU fan motherboard plug. Maybe you can check the fan connections to make sure they are plugged in properly and being controlled by the motherboard.
As for the USB wake options, maybe your motherboard simply doesn't have this feature. Some older motherboards may not have this capability, and wake options for serial ports and PCI devices are more common. A USB device is technically considered a communication device, but it's not always listed as such in the BIOS.
Regarding the "F2 thing" you have to hit for the computer to start up, this is likely a setting in your BIOS called "Quick Boot" or "Fast Boot." Enabling this setting will bypass some of the initial startup checks and allow the computer to boot up more quickly, but it may also prevent you from seeing certain messages or options during startup.
Finally, regarding hibernation and sleep, these are two different power-saving modes in Windows. Sleep mode keeps the computer running in a reduced power state, while hibernation mode saves the contents of the computer's memory to the hard drive and then shuts down completely. When the computer is turned back on, it restores the contents of memory from the hard drive and resumes where it left off. Both modes can be useful for saving power, but hibernation mode uses more disk space and takes longer to start up and shut down.