@rkorell finally I got it solved :)

The issue is really the GPIO numbering, I found this SO thread:
https://stackoverflow.com/questions/78173749/use-raspberry-pi-4-gpio-with-node-js
It is also valid for Pi3 and Pi2

cat /sys/kernel/debug/gpio

gpiochip0: GPIOs 512-565, parent: platform/3f200000.gpio, pinctrl-bcm2835:
 gpio-512 (ID_SDA              )
 gpio-513 (ID_SCL              )
 gpio-514 (GPIO2               )
 gpio-515 (GPIO3               )
 gpio-516 (GPIO4               )
 gpio-517 (GPIO5               )
 gpio-518 (GPIO6               )
 gpio-519 (GPIO7               |spi0 CS1            ) out hi ACTIVE LOW
 gpio-520 (GPIO8               |spi0 CS0            ) out hi ACTIVE LOW
 gpio-521 (GPIO9               )
 gpio-522 (GPIO10              )
 gpio-523 (GPIO11              )
 gpio-524 (GPIO12              )
 gpio-525 (GPIO13              )
 gpio-526 (GPIO14              )
 gpio-527 (GPIO15              )
 gpio-528 (GPIO16              )
 gpio-529 (GPIO17              |sysfs               ) in  hi IRQ
 gpio-530 (GPIO18              )
 gpio-531 (GPIO19              )
 gpio-532 (GPIO20              )
 gpio-533 (GPIO21              )
 gpio-534 (GPIO22              |sysfs               ) in  hi IRQ
 gpio-535 (GPIO23              )
 gpio-536 (GPIO24              )
 gpio-537 (GPIO25              )
 gpio-538 (GPIO26              )
 gpio-539 (GPIO27              |sysfs               ) in  hi IRQ

I needed to set up the numbers according to the output
e.g. Pin27 is 539 in the MMM-Navigate config.
Now everything works so far as expected, thank you all for your help!