I quite liked this game, very unique concept and story! While the game was a little clunky and unwieldy at times, I still quite enjoyed it. The only issue I had with the gameplay was that the spirits seemed to "ignore" Mokou's flames a few times, particularly when they just finished moving or when they were about to move. I also had a game crash at around level 20 I believe (it was the room with the karakasa-obake, fairy, and spirit), right before I was about to complete the level, which was a little frustrating. Also, on level 10, there appears to be a second "exit" near the start of the level, which doesn't do anything but make Mokou and Keine play their "leaving me behind" dialogues.
Would this game have been smoother had it been made entirely in Godot? Maybe. But for what it's worth, I think it's much more interesting for this game to be made in something like RPGMaker. Admittedly, I don't play a lot of RPGMaker games, but I almost couldn't believe this was one until I saw the pause/retry menus. You've stretched what this engine can do (perhaps literally, seeing as my browser was threatening to blow up on me towards the end of the game), and for what it's worth, I think that's awesome.
Speaking of awesome, I really liked the narrative in this one. Mokou's plight reminded me of a vampire's (of which I have a slight fascination with), and her struggle was very compelling. I don't often read stories dealing with Mokou's existential crisis about being immortal (mostly because I'm barely keeping my own existence together), but I truly enjoyed seeing her admit to caring about Keine and wanting to be with her, no matter how finite the time they share is. Keine never giving up on Mokou, even when she was a human, is pretty sweet to see as well.
Like I said in the beginning, this is an epic game with a unique concept and compelling story. It's a bit rough, but I think that roughness just a product of how incredible the gameplay could be, yet how it is now is almost a testament to how much effort was put into making it work. Great job!