It shutdowns ok with SSH or from GUI. The only thing is the red LED that still keeps turned on preveting me from turn the Rpi again back on after shutdown - I have to manually press the button for few seconds.
I have a feeling, you want something what's never existed.
I have 3 RPi's and using with LE for years. And the red LED after shutdown always remains on, and to start again always needs to do a power cycle. That is how the RPi works with LE. It's not like a "normal" PC, with stand-by part in power source and with IO chip always powered, ready to react if the power button is pressed (and with a hidden power consumption in stand-by...).
The RPi have only a single GPIO input able to force to boot again if is activated with a button.
If you have concerns about the "LED red light", I think that LED can be disabled in config.txt.
If you have concerns about power consumption, after RPi "shutdown", the most part it's the power source itself (like any phone charger, have some consumption even if no phone connected), so switching of the main power can be the solution.