It was only because they didn't have the budget to build several different models; that is, until the Vor'cha model was built
Though I generally don't like tampering, part of me wishes the new TNG-R versions of these episodes will swap the oversized BOPs with Vorchas or Negh'Vars or something.
For "Yesterday's Enterprise," they couldn't use Vor'chas or Negh'Vars because the dialog explicitly stated that the attacking ships were K'Vort class. Therefore if any CGI updating were to be done, a new ship type would have to be created.
And for "The Defector," they couldn't use Negh'Vars (a ship comparable to the warbirds in size) because the Negh'Var class hadn't been created at that time.
However, I don't think we're going to see anything except the original footage of either episode.