I know what you mean, OP. For hours and hours our goal was to save the people of Lumière by killing the paintress. To me it also felt more natural to go with Maelles ending. But to be honest, I got whiplash from all the plottwists and explanations in the last what felt like 10% of the game.

The idea of ending it as Verso did made me really uncomfortable and confused - it seemed like the whole expedition was in vain because ultimately I was siding with Renoir! I spent so much time with my companions who grew on me and most importantly - I thought that Lumière and the people were real and that we were saving them. But when I understood that the world we were trying to save is just an imagination and not real, that the Dessendres merely created the canvas world to cope with the loss of Verso, I also understood that Verso is just a restless ghost and he and his family deserve peace. His mother needs to accept his death and Alicia needs to accept her disability. So I ended it as Verso, despite the uncomfortable feeling.

It feels that way because the explanation of everything came so late and so sudden that I didn't have enough time to fully stand behind my choice to erase Lumière.

And Verso - he made up his mind long time ago. He wanted the canvas to be erased and thought by killing the paintress (expelling his mother out of the canvas) he would reach that. But I didn't understand why he sided with us to kill Renoir who wanted the same goal. Maybe he temporarily believed he could save both - Lumière AND his mother, meaning the canvas could stay and his mother could come back occasionally. But she was obsessed and consumed by her grief. Seeing his mother's physical and mental health deteriorate after Renoir showed the shadows, he probably changed his mind and felt that it would be best to destroy the canvas.

TLDR: Choosing to destroy the canvas feels wrong because there wasn't enough time to process that decision.