Might be gravity manipulation would involve "changing the setting" by summoning incredible forces of nature - after which the setting would remain changed until further application of the forces. That is, gravity is forever, even on an otherwise dead starship, unless you shock it with the energies of two photon torpedoes...
A lot of Trek seems to assume that currently assumed laws of nature, especially as regards the more fundamental ones on conservation or balance, do not apply: something is made of nothing, or nothing out of something, willy-nilly. It might be all this becomes possible when something gives - if one learns to change the setting on inertia without needing to flip another setting elsewhere for balance, all conservation laws may break down, and transporters and warp drives suddenly become possible.
Then again, subspace. If one enjoys access to parallel realms, one can dump stuff there to break symmetries in our native realm. Subspace might be a (theoretically or at least practically) bottomless sink of momentum or charge if need be. Or the famed phased realm is. And make-disappear guns might be but the very coarsest application of the dumping process.
Timo Saloniemi