Why is Monika's NEP limited
The world of "Doki Doki Literature Club!" is made of datas that make up its entire existence and all the aspects of reality, as stuff like plot, time, mind, memories, etc. are all just data files that can be manipulated.
Singular entities are no exceptions, as they have their own .chr files, which can be altered, causing the being to also be altered in return. And if you already have guessed, deleting a .chr file deletes the respective being from the game, causing it to not even having existed in the 1st place as the game would literally reshape itself to patch up their lack.
Monika also has a .chr file. The reason behind her NEP is because she can survive just fine without said file and act normally even after her deletion, for her the file is just like hair: unnecessary, but painful if removed, but it's
Limited because she starts with her existing as a .chr file.
and what does she start with?
The most offensive thing she ever did is deletion, which, as I said above, erases one's file, causing them being erased from the game itself, causing their file, concept, information, history and narrative to be erased, with the game reshaping itself to patch up their lack, making the character to have never existed in it (meaning you'd need literally all the aspects of High Godly Regen to recover).
And yes,
that stuff is thought-based, she just needs to delete Rimuru's .chr file
from the "characters" folder.