It makes no difference to the TOC's accountants, as unlike airlines or coach companies, TOC's sell tickets (especially season tickets) on a "turn up and travel" basis.
If 500 people want to squeeze onto the 1800 to Anytown, then they can and will get on whether there are 400 or 500 seats, and the TOC will get the same money regardless.
However, if the TOC has arranged the seating so there are 500 seats on board (rather than 400 in a less efficient arrangement), then there is more chance the 100 passengers who would have been standing will sit and have a more comfortable (and some would argue, safer) journey.