Agreed. Someday I will watch that fanedit as a thought experiment. But while I've heard quite a few people suggesting an extended cut for broadcast I don't like the idea. The Missing Pieces are cool as curio fragments (I also like them as a bridge between show & film but seem to be alone in that). Some are as good as/better than certain scenes in the movie and a few would not feel out of place back in it. But by and large FWWM is the movie it needs to be and an late age version would inevitably dilute it's intense, claustrophobic aura. Also, it is a moot point because Lynch is extremely stubborn about sticking to final decisions. I don't think he would even "fix" Dune if give the chance. Which is also what a s2 recut would never happen.
I wouldn't agree with the idea that Lynch is really that stubborn. He did add little things to FWWM before, like the different fadeouts with Desmond, the monkey audibly saying Judy, etc.
In addition, I know a Russian fan, who claims to have a seen a TV broadcast of the extended [likely workprint] FWWM over 20 years ago - she didn;t know it was a movie, but an extended episode (the Desmond fight was in there). I wouldn't put this up as implausible - Russia had a huge pirate market, and many workprints, screeners, etc. tended to leak at the time, usually on VHS.
In the case of Dune, I've read an interview from the 80s, where Lynch openly talks about wanting to release a 4-hour cut of Dune on VHS, claiming the theatrical version is "too short." This, however, was shortly before the film's infamous TV release, which suggests that the TV cut was what permanently turned Lynch away from Dune.
Now the impression I get is majority positive. I think The Entire Mystery may have been the tipping point to to a cautiously positive shift in the conventional wisdom about FWWM. There's still a fair amour of negativity out here but the balance has shifted subtly toward "it's underrated"/"best part of Twin Peaks"/"powerful depiction of abuse"/"love the David Bowie craziness" (the praise comes in all forms).
The thing about the box set is that it reframes the film as part of the whole TP experience - and really, it's always played less as a standalone picture or even a prequel, than an extended epilogue that builds on a lot of the show's mythology from the first two seasons, even though it depicts what happened before.
This is a structure that, at the time, was practically unheard of when it comes to television. Now, a lot of shows do it.