What an incredible experience! While I thoroughly enjoyed the game, I'd like to offer some constructive feedback for even greater enjoyment. There are a few easy adjustments that could significantly enhance gameplay.
INVENTORY
Firstly, the game's mechanics feel somewhat tedious at times, detracting from the immersive experience. Streamlining inventory management by consolidating pop-up screens and allowing batch selections would greatly improve flow and reduce unnecessary clicks.
I would condense the popup screens into 1. No need to ask me every time if I would 'like to access x machine'. You could include the description of the machine and what it does along with the interaction popup. I think you should always try to reduce the numbers of clicks a player needs to make. That also means making it so that you can select 'how many' flasks/beakers you want instead of making the player re enter the flask storage for each individual flask.
CONTROLS
Regarding controls, perhaps by eliminating the need for additional key bindings like 'E', it would enhance accessibility and intuitiveness. Simplifying controls to basic WASD and mouse interactions would be a bit more straightforward and require less controls.
UI
Additionally, I would make the inventory UI 'jump over' to display closer to the popups instead of needing to drag all the way from the top left to the popup and back.
I wouldn't rely on using 'darkest color' as an identifier for which flask to keep track of because some people may have color blindness that would automatically make it hard to distinguish which flask they should be tracking.
Overall it was a great entry! I had a lot of fun and it is really well made! Great work!! :D