Considering the weight considerations and potential for disaster (as in the end of STRANGERS ON A TRAIN) with an out of control gimbal or motion base, or even a runaway motion control rig like the Image-G Bulldog if it ran amuck, (it operated at real-time speeds for shooting live-action, flying right up to the cockpit window of the Mars Recovery in MISSION TO MARS), this idea doesn't sound anyway near as dangerous.
Specific to this, from where I stand, is that the probe pretty much, with only slight changes, runs in a circle or oval, which ties in with the cutting a one- or two-slit approach for the overhead rigging. It could have been hung off a crane like the BoP bridge was in TVH for its tiltawhirl moments (though to be fair, TVH's physical fx guy was top-of-the-line, which I don't think can be said for TMP's guy, who seemed to have problems even with getting the doors to open.)
There are practical lights installed in it (not talking about the ones in the soffit round the edges, but a series of I think 3 holes that in the ceiling, probably behind the captain's chair) I think in TWOK or SFS, so cutting into it would not damage it (if it were so flimsy, they wouldn't have been able to clear installing it overhead for the same safety concerns you cite, especially given that it contains stuff that is probably motorized or blockNtackle driven, like the astrogator/tilting dome thing.)
Anyway, with the path of the thing limited to arcs, you could keep it from getting too close to actors or other obstacles in wide shots, and you could do whatever cheat you wanted in closeups, putting it on an ironing board or whatever. Plus, running the power out of the set from above would have stepped around some of the teeny danger of an on-set electrocution or short-out, which would have been possible given that some metal was in the sets.
Just another example of the Proper Planning Prevents Piss Poor Performance aspects that (for me) plague a lot of TMP (and to be fair & honest, parts of TFF as well -- Mike Wood's rig for the turboshaft sequence is a modest miracle given time & resources, but the scene does not bear close scrutiny at all, & I ain't talkin about the deck numbers.)
The 6P thing jives with my views on other TMP lamebrainedness, like lowering the wattage on internal console bulbs from, what, 25 watts to 6watts, to keep the buttons from melting, reducing illumination 75% on the boards, instead of getting better plastic buttons or cutting them out of plexi or putting some more fans in the consoles.
And the high-concept notion of the art dept, to have most illumination coming from the floor, while it may look good in theory, is extremely unfavorable to actor faces in practice, and pretty nonsensical when it comes to reading a report, unless you sit upside down in your chair and put your feet up over the captain's headrest to scan the clipboard. (there's probably some good psychological reason you don't light from the floor too, like it messes with your balance or something, because it doesn't look so much futuristic as it does look WRONG.)
As for the Trumbull notion of flying a physical saucer overhead, I don't see how that differs much from what Dykstra did in LIFEFORCE by rigging a 10K or some monster light to fly over the streets of London set with all those extras underneath it.
Of course, I guess you could say that was an example of British craftsmanship (it's what I would have called it in the old days), but these days, when I think British, I think British Petroleum, and that's more like crapsmanship, especially now that I've started hearing about their part in the EXXON VALDEZ, and how THAT mess could have been quickly contained if BP's supposed nearby cleanup equipment and vessels ACTUALLY EXISTED instead of being so much vaporware, apparently owing to BP practically owning the political bodies and half the terrain in Alaska. Just something I came across on public radio recently, from a guy who spent years of his life doing the official investigations and whom I guess no longer has any gag orders in effect. Sorry for aside, but it just leapt to mind when I was writing this & I haven't had a chance to mention it to anyone yet.