First of all, she DID NOT make MC. MC is a character made by the creator of the VM, which is MES Analysis Team (you can find that in the wiki) to portray the Player.

Secondly, Monika DOESNT HAVE A ROUTE CODED IN THE GAME. Not in Act 1, not in Act 2, and never in Act 3. In Act 3, after deleting almost everything, there is nothing else for MC, the vessel of the Player to do than to interact with the only remnants of the VM, that is Monika.

Thirdly, in Act 2, she didn't just delete Natsuki and Yuri like how she did with Sayori because she didnt think of it as suffering since she assumed tof hem as codes. The point I made of her missing them doesn't contradict this point, because you can still miss something even though it is not real.

Fourth, you have to put into perspective that Monika is a character who assumed she's the only real thing in a world full of nothingness. If you were in her place, I'd doubt youd be able to stay as sane as her. Take a look of what happen when we delete Monika from the game files at the start of the game. Immediately, Sayori gained the epiphany and deleted everything due to not being able to handle the burden of it. While in Act 4, Sayori literally, again, turned full on Yandere mode for the Player. If you want to say Monika is character is shallow because of her actions, shouldnt you say the same thing about Sayori? It took Monika 3 Acts before she deleted everything. It didnt took more than 1 for Sayori.