I've been playing with MGE lately and noticed that it doesn't change the water for interior cells. Is there a setting related to this? More to the point, can I ensure that my mod's interior water uses a particular MGE shader regardless of the user's MGE settings or third party water shaders?

Yes and no.
To use interior water, you need a few settings turned on (interior distant land and such) and a newer build.
There's no way to force a particular water shader, since there's only one in use at a time (only one installed).