The shutdown command will not turn off 5V completely - it goes to standby. In standby it will listen to GPIO, and can be switched on with a GPIO button.
I have been installed a power on/off button at my RPi3B+, which works perfectly with LibreELEC. Read this thread for instructions. If I understand you right, your timer will do a complete 5V power off after the shutdown.
PS: With the off-button.py script (see linked thread) you can trigger a GPIO signal right before shutdown. If you listen to that GPIO "off" signal with your timer, it should work.