The "BLheli bootloader" is small configured AVRootloader:
Proprietary serial protocol.
Fast speed, needs only a simple serial PC connection at least.
Small size: only 512 bytes.
Can write Flash memory and EEprom, but can only read EEprom (read Flash would increase the size to >512 bytes).
Does not wait for Throttle low until it starts.
The SimonK Bootloader is a type of STK500 bootloader:
Protocol: Subset of STK500v2 protocol.
Speed is slower than with AVRootloader, needs a special programming stick like USBLinker or AFRO USB.
Larger size: 1024 bytes.
Can write and read Flash memory and EEprom.
Does wait for Throttle low until it starts.
If the SImonK Bootloader would be as small as 512 bytes, I would prefer it over the AVRootloader. With SK Bootloader all MULTI Hex files fit but it is to big for certain MAIN hex files.
There might be other advantages of AVRootloader, if using PWM as input signal.
HTH