Thank you so much for giving the ROM a shot and for taking the time to write in quite a lot of detail!
...
regarding the physics: yes, the player sprite is 16 pixels (2 tiles) high, and the interaction coordinate is anchored to the character's head/upper tile rather than their feet. for us, at least for now, those are technical constraints of GB. so, if you line up by your feet, the interaction check can miss by one tile. Aiming with your upper body will make interactions trigger reliably
quick tip for the rest of the game: whenever an object says "hands find nothing" or gives erratic readings, you can press SELECT to try another instrument. Later on, you'll unlock additional tools (a Polarized Viewer for hidden microfilm/ink, and an Alignment Anchor for rotary mechanisms)
hope this helps you dive into the rest of the cartridge! we see that the colleague, bulbacon, has just added a tip on how to pass the first screen. let me know how the rest of the run goes.