Well what do you know. I measured the other movie.
On the gem pedestal, if you up&a after losing control of link but before the gem is actually in the statue, it removes the gem from your inventory, but the statue is still active. For some reason, nobody has thought to check if you could place another gem after this situation has arisen. If, however, the palace item is collected and the gem is fake-placed, the palace still turns to stone and you can't return. Great Palace only requires that you have 0 gems left to place, and so you can skip bosses.
The obvious use of this is to place the gem in Palace 1 multiple times to save time elsewhere by skipping bosses, notably the boss of Palace 4, which requires a lot of preparation. However, if a required item is skipped, a gem can be placed multiple times in any palace-- except Palace 2, which requires the palace item to reach the boss. Thus, technically any gem is available to exploit, if it saves time. For completeness' sake, all gems will be considered for exploit (besides Palace 6). You could skip an earlier boss and double P6's gem, but it takes nearly as long to walk to P6 as to finish P1, let alone the gem altar, so I won't measure. Frame counts are considered approximate; small changes to exact overworld path, key collection, spell queueing and level-up dialogue boxes will change these slightly.
Reference movie for timing:
[3254] NES Zelda II: The Adventure of Link "warpless" by Arc, FatRatKnight, Inzult & Rising Tempest in 45:26.04
Below is theoretical time lost for doubling up on gems, ignoring boss fights. Counting from the start palace, since doubled gems should always be from (or include) an up&a and thus always add that time. All counts in frames.
Time spent doubling Gem:
P1; 7,236
P2; N/A (Glove Required)
P3; 10,475
P4; 11,313
P5; 11,033
P6; N/A
Below is theoretical time saved for skipping bosses/prep. Obviously, skipping a gem means you can't also double it. For P4, the time collecting the kid and Reflect spell must also be considered and has been added. P6 can be skipped, however, Old and New Kasuto still must be visited and as such the overworld route is basically unchanged.
Time saved skipping Gem:
P1; 7,692 (No need to visit)
P2; 7,215
P3; 5,307
P4; 10,158 [kid quest] / 6,545 [gem skip]
P5; 6,502
P6; 9,995 (No need to visit)
So, with P1 being so quick to double, it's the only real option. I was thinking P3 might be more competative, but it is too slow. For P2, estimates put it very close whether skipping the boss is worthwhile, and thus would have to be tested more exactly. P3 and P5 bosses/gems should not be skipped, as they are close enough to the required items to be worth the visit. Since P6 can be ignored, and P4 takes so much prep, they should be skipped.
The route becomes: finish P1 3 (or 4) times, finish P3 and P5 (and maybe P2) while getting the items. This does affect the leveling, particularly magic. Since there are no longer 4 doors in a row to pass in P4, it doesn't need to be rushed as quickly. Magic-5 is still required eventually, possibly for Palace 5, and definitely for Thunderbird. For P5, with 7 bars of magic even at magic 3, timely blue jars and/or death abuse should be enough to get through. This aspect would take some closer examination.
As for the other movie, it should be measured separately, since some routing is different. I suspect it would math out more or less the same overall, though.
Whether or not this exploit is good to use in both or either run is a separate question, and I welcome opinions starting... now.
eta: i think skipping the P5 boss saves even less time than listed, since it would add an extra up&a and trip back to East Hyrule at ~1,600 frames.
So in warps, we can get it to 1 after the refill on the way to the flute, then 1 on the way out, then a refill, then 1 on the way to gooma.