Sometimes you have story-related fixed encounters with some creatures where you cannot change the creature type. If needed because the encounter would be too low/high for your party you buff the challenge rating of the encounter, not the creature type. Pretty sure you already found that in some PNP campaign you already played, you just don´t know it because it´s something that only the DM knows.
I mean, if you are supposed to raid a greenskin fortress to kill the goblin king you cannot change it and create a fortress full of lizardfolk and make the goblin king a beholder just because...
I get your point about story-related fixed encounters, but you can take difficulty into account by saying "if medium difficulty, leave as designed. If hard difficulty, add in 2 extra x, if very hard difficulty add in giant". You don't have to completely change the fixed encounter creature type, you can just add more or remove some.
