Hey you volunteered for some in depth feedback so this is on you. Also please note that I am generally not into puzzle platformers so this is all coming from someone not in your target audience. Also note that my submission has a big list of it's own issues. Anyways here's what I would personally adjust if this was my game and I had infinite time.
Game Page & Title Screen
First just the game page, you have one screen shot no gifs no art. I would take gifs of either jumping or placing the box down or some other simple gifs showcasing the different mechanics you have. As it is, the game page is very plain and unattractive.
The color scheme in the title menu and the game in general clashes pretty hard. Outside of just learning color theory, you can use adobe color or some other tool to pick colors that work together better.
I like all the settings possibilities and the ui in general, but the outline box is a bit ugly. Instead of the outline box for buttons, I would make the default font a little darker on the text and just highlight / scale the text. I think it would make the entire UI look a lot cleaner with the same amount of work you already put in.
Controls
On one hand, you picked really good keybinds. Every keybind makes sense and is familiar due to other games using same keybinds, some people in this jam should take a lesson from you on this.
Anyway my biggest issue with the gameplay is controlling the character. You walk way too slow by default, I would remove the shift key, make the default speed the run speed, and probably make the rooms significantly smaller as well.
For the interaction I would have a toggle for carrying the boxes, press E to hold box, press E again to drop it. Jumping into platforms holding a box doesn't feel good as it is. Also dropping boxes is difficult and finnicky, I would try to make them weight significantly more, and if that doesn't help I would have them drop into slots that they click into place in.
Level Design
Second reminder that I don't generally play puzzle platformer games, you may get better feedback from someone closer to your target audience.
The rooms are too big and too plain. Walls desperately need some simple texture and a cleaner color scheme, floors should have a separate texture as well. The room being so big makes it really difficult to see what was happening with conveyer belts and anything else and it just feels weird to walk around in, I believe that having the puzzles be more concise would generally improve the feeling of the game.
The starting puzzles were all really simple and repetitive, there was no thinking involved and there was no new puzzles for multiple levels. Also it is my firm belief that every puzzle game in game jams should have a skip level button, so people can experience the entire game and don't just quit when they get stuck.
Anyways I am always impressed seeing 3d games in short form game jams. The design of the cube was really high quality, and I'm a big fan of the infinite room theme!