... is it the creator's sincere belief that overhead Atmos effects should be absent or is their absence more a function of (1) budget/time constraints, (2) studio ambivalence (do it this way, no exceptions), or (3) mixer's inexperience?
I don't think there's likely a straight answer for this I'm afraid. To those three points though, I think point (1) may carry some weight. If you're working in Atmos, in many ways it's just as easy to put FX in the overheads as anywhere else, but since working in Atmos is slower than 7.1 (despite what Dolby may tell you, or me) a view is still sometimes taken to effectively prep, tracklay and maybe even do some premixing in 7.1 and treat the "Atmos" element as an upmix in the final mix (i.e. at the end of the sound post process). I don't like this way of working, but sometimes it's just what happens. This workflow obviously lends itself less to overhead use, as once you've got something working in 7.1, picking up some FX and throwing them around the overheads can quite quickly break the integration of the mix, so there is more chances things will be left at Z=0 (i.e. ear level).
As Atmos becomes more commonplace, more and more films are being done "properly". That is to say, we're doing ever more in Atmos from the get-go. So I think, over time, things may settle down a bit in regard to overhead use.
I'm not sure studios (2) dictate this; certainly I've never been asked by a studio to do anything specific in this regard, although some studios do tend towards quite a small pool of mixers who may lean towards less overhead use, giving the impression it's at the studio's request?
To (3) inexperience; I don't think so. If anything, I suspect inexperienced mixers are more likely to throw sound around than the more experienced ones. I say this because I've worked alongside both (I still consider myself somewhere in the middle!) and generally the inexperienced treat it like it's their job to create ear candy, whereas the more experienced have the confidence to craft something that, while sonically pleasing, is simpler and more biased towards delivering emotion and support to the story than short term wow factor.
Some of my own thoughts on this are along these lines:
I think a big factor often overlooked is the cut of the picture, which we really have to follow because it's weird to put stuff overhead without visual reference to it. To break that down: (1) in the first instance, obviously some films (your MI example being a good one) have lots of opportunity for overhead use, whereas a lot of films happen at ground level and apart from the odd forest or rain scene in a metal roofed building etc, nothing really happens overhead in picture. Even in an action movie, if the camera follows everything that happens and keeps it centre frame, rather than things happening around us, we don't have as much opportunity for [obvious] surround/overhead use (2) That aside, little things, like whether the editor/director cut away as soon as something goes out of frame or hold on that shot for a half a second or so afterwards, make a big difference. Take a helicopter flying overhead; if it flies to camera but they cut away as soon as it reaches towards the top of the frame, there may not be much opportunity to put it's sound in the overheads, depending on where we go on the B side of that cut. If they hold the A side of that cut for another 12 frames (or more, whatever!) of course the sound can track it's movement out of vision. Or maybe, using the same example, the camera moves to follow the helicopter and it never actually goes properly overhead. We still might cheat a bit of overhead in, but it won't go full tilt. (3) If the film is 98% happening in frame, then even if there is a brief moment of action [for example] 40 minutes in where the overheads could be used, we may shy away from it more than if the film had established itself like that earlier on. Otherwise, it's a sudden moment of "Oh, we've got overhead speakers" followed by "oh, they've gone again"
Also the director (or whoever's at the helm at the time of the mix!) may be afraid of sound effects in general... They've become used to hearing their film in stereo in the cutting copy, where they've just got some commercial music instead of their score, a few crappy sound fx put in by the picture editor, and the dialog. Suddenly, they're sitting in a cinema sized room, we're throwing new stuff at them, and they can get freaked out if we're not careful. FX playing from the overheads is likely more separated from the rest of the mix to them, and they're more likely to ask us to remove it because they're not used to it. My suspicion is, when you've got a director like this, more fx will survive elsewhere, not because they specifically like it, but because it doesn't grab their attention so much - or at the very least - it's a more difficult note for them to give us because they don't know what to say!! I'm actually unsure, even on my mixes, how much of an overall effect this has. (I will add though, I don't mind a director culling sound effects, regardless of panning, if it makes the story telling better!)
Lastly, there's bound to be an element of personal preference; be it the mixer's, the supervising sound editor's or the director's, and there's probably little standardisation of personal preference possible... I think overheads can be perceived as distraction unless the picture specifically shows us what's going on, so outside of that scenario, there's quite a fine line of density vs detail that has to be walked. I.e. the more sounds you have going on, the less "focused" the mix is. And it's a preference that has always existed in all formats, I guess it's just more obvious to talk about it in terms of overhead use than LCR or surround. If someone's pre-disposed to a less dense mix, that will translate to less overhead use of course.