No Replay(+quote) option in this forum... but I'm very sure we understand each other.
Lightroom thumbnails: yes, I believe you. But, on my average PC (Intel E8200) I can hardly notice that (must happen for very short time).
I'm with you, when you say, all parameters (thus, incl. thumbnail) should be updated as well. On the other hand (to keep that word), then you should embed new (modified) thumbnal instead of existing one.
And to make things worse, there might be two different thumbnails inside CR2 file:
1. 160x120 "thumbnail of CR2" -this is "main" thumbnail, so to speak.
2. 168x112 "thumbnail of JPG" -which is embedded into preview (jpg) image.
I said, there "might be", because newer EOS cameras (5Dmk2, for example), doesn't have that second thumbnail at all. For reasons like this, I gave up on thumbnails.
Viewing CR2 (in Faststone, etc.)... There are two basic options:
1. Viewing actual raw image (converted by Fastone),
2. Viewing embedded jpg image
-in both cases, only Exif:Orientation tag is used for correct orientation. DPP does opposite: it only uses CanonVRD tag. And RAW-data remains unchaged all the time anyway. I don't see any troubles here (I mean, the way GUI does that).
Of course, it can happen, GUI may not embed image with orientation expected by user. But I see those as special cases -GUI is ment, well... for "everyday" use :-)
As for special cases: they can be solved only when using exifool "pure" :-)
I don't think our approaches differ much. I'm trying to make "best possible" too, as long "I see" it's worth to bother -and there's enough time to do it.