Really interesting submission, reminds me of a idea I saw somewhere for a tesseract based dungeon where there were only 6 rooms but many, many ways to get to each one and depending on how you got there the gravity would be different... (if I find the link I will post it.)
Interesting things could be done with 'reverse weight' equipment (armor anyone? Or combine materials from both (say, in forging metal or just mix components and get a zero weight item) and certainly I foresee lots of interesting cultural interactions (PC's start up a embassy?) Pick a culture that is interesting enough in its own right that does not have a analogue in your setting, and work your way up from there. The 'gravity issue' is a interesting cultural barrier where communication is possible but there are still issues...
...what happens if people from this world and the other one have children? Zero-gravity babies? Or does the baby pick up the 'gravity' of the mother (which makes sense in a matter-based system of tracking)...
...though if its a matter based system of tracking, visitors spending enough time on the other side and eating the food will eventually switch orientation. Which could be cool. Especially during said zero-gravity transition period. This works well on a world that has been canonically declared 'flat'.
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P.S. I think I found the original article, for those interested. I say 'think' because I remember a more clearly laid out map of what the rooms would look like connected together. It was Dragon Magazine, issues 17 and 38, or both in the Compendium. Gravity was subjectively consistent (no reversal of gravity doors) but objects (or creatures) in the room could have a different gravity then your own, based on how they got to that room.
The Good: A highly adaptable open ended plotline full off choices and consequences, interesting NPC's and fun tech to play with. If this entry is short, its cause its fairly well rounded.
The Bad: Explicit Doom references (this is forgivable). Also, in the 'Artifact Recovery' choice, in that position I (as a PC) would be inclined to possibly fight my way to the artifact and try to disable it from there, using the enemy EMP would not be my first thought. A good DM can improvise on the spot, but its a hole in the options provided. Not a glaring one though.
I really wanted to like the references, but in the end I had to admit it distracted, and pointing them out was unnecessary to the submission. Still, good job plotting out a lot of the ways it could go.