Hello Igor and thanks for your response.
It is still not entirely clear.
In my case (using MCIMX6Y2DVK09AB) I have a I2C port multiplexed with 2 of these configuration pins.
Now I2C requires pullups to VDD, value depending on I2C speed and line capacitance, but lets says around 3-10k.
If the required boot cfg value is high, then all OK.
However if the required value is low, then the 10k resistor to ground will be installed, but there will still be a pullup to VDD through the series combination of the isolation resistor and the I2C pullup.
I would appreciate if you could consider this case also.
David