I am answering my own question. The way to force Knot to resolve locally a fqdn domain is to add the following line to the custom configuration file:
line:
hints['mon.sous.domaine.fr'] = '192.0.2.18'
in:
/etc/kresd/custom.conf
The answer can be found more or less under different posts in the forum. None of them seemed very clear to me, some of them seem to confuse the hints directive with selective forward to a particular DNS, depending on the domain. Perhaps this short, more explicit post will be helpful to some. Or perhaps it is me who has not understood the deeper implications of the hints directive. Either way, it works for me.
This is where you can find the official Knot documentation page on the subject. It is easy to find… once you know the answer.