I have noticed that some HETATM records are read by Modeller and
automatically handled as corresponding standard residues (for example
MSE -> MET)
Actually MSE -> MET is the only such translation done.
I would like to know if you could suggest a way to disable this
behaviour and really ignore all HETATM records.
Unfortunately there isn't any way to do that - it is hardcoded into the
PDB reader. Why do you want to treat MSE as HETATMs anyway? There may be
a better way to achieve your goal.