Thanks! It means a lot to me that you've gone into so much detail.
It's intended that you're able to skip levels by smuggling items from earlier levels. That being said, it is possible to beat Pluto's third room in 6 snapshots without smuggling items (or abusing the physics engine).
I like your work-around for the jetpack revert puzzle! When you revert a snapshot that involved you picking up an item, the item will go back to its original position. To avoid this, take an extra snapshot after you pick up the jetpack but before you use it.
The rule about dropping items in a Merge is that it depends on the snapshot where the branches diverged. Here's an example:
Since I'm carrying the key in Snapshot #1, the game will focus on the fact that I dropped the key in the top branch, so I wouldn't get the key in Snapshot #6. If I wasn't carrying the key in Snapshot #1 then I would be carrying it in Snapshot #6.
I hope that made sense and that you can apply that explanation to the trophies. Good luck!