As bealzebub and Schmoogle said, the MTOM calculation SHOULD take that all into account on the loadsheet, so if your 'loadmaster' is not doing that he/she will trip up in any case at the loadsheet stage - and should be shot or hung by the neck.
In my experience most trip plans assume cont to have been burnt at touchdown.
In any case most wise pilots always reduce trip fuel by x% for MLW calculations anyway in case the route is shortened or winds/levels are BETTER than planned so as not to arrive 'overmass' as I believe I have to call it now