I'd like to thank you for the highly constructive comment - it's genuinely helpful and I appreciate you taking your time to write it.
The box puzzle was intended as an alternative way into the church, in the vein of many immersive sims where different problems have multiple solutions. ATROPOS was my first real foray into this style of design and it's flawed in multiple aspects, many of which are evident even just in the different problems you pointed out with the boxes.
Apologies if you were frustrated with the limitations of the game - I was as well. I went on to make RADIOTOMB during a future game jam and I consider it to be an evolution of the ideas I first experimented with in ATROPOS. I'm fascinated with immersive sims and survival horror so it's definitely not my final examination of the genre, there's more in the works that I can hopefully release in the future.
Thanks again for the valuable review and I hope you enjoyed some elements of ATROPOS despite all of it's shortcomings.