Yes, perhaps difficult variations should affect base value and GOE should be reserved for how well performed the jump was in all those aspects and height, distance, flow, speed. The only problem I can think of is that it could get quite complicated to score each jump because how would the BV be determined? Are all "difficult" entries/exits/variations created equal (add the same amount to the BV) or are some more difficult than others? Would it be similar to the bonus we have now with jumps in the second half of the program being worth more? Would skaters have to submit the features they plan to do in a planned content or something like that?
Yeah the actual details probably would be complicated.
My personal vote would be for each entry, exit and arm variation (and maybe delayed rotation?) have a specific bonus in a table basically (ideally scaled to the number of rotations in the jump). I'm sure that determining the exact points would be a lot of work for the ISU (as I imagine was determining the score associated with each jump) but once it was done, it would be done minus tweaks in scoring. Debates about how difficult a tano is would be about the number of points they added, not about whether the judges had counted them or not when awarding GOE which IMO is preferable since it could lead to tweaking to those scores as opposed to now when all there is is whole scale change every quad and memos
You could certainly have them submit it in advance but they could also just look and see whether any of those elements were present. Do they submit their planned steps or spins for each sequence in advance re determining the level (I looked on google but didn't find any easy answers)? Which ever way they do it, I'd vote for being the same thing for this.