Don't you love it when that happens?

The Federation almost perfected it, except the power requirement was too strenuous. The device was ahead of its time.
That probably is a factor in why the Federation agreed to stop. If an official prequel actually filled in the gaps, the time and effort to think up all the nuances and resolve those without introducing new problems is a tall order.
As for intelligent molecules and atomic structure for each object involved - yeah, gaseous matter vs solid begs questions - especially the latter. How does the gravity plating work as opposed to rotational forces, like in 2001 and other movies that explore artificial gravity? This could explain, in a small part, how they can remain relatively attached - but still get pushed out through the exterior hull... not to mention, would phased matter outside be drawn to the same plating? (Or perhaps not, the field is localized and calibrated already.)