Even believing that Shanks' Sword Gryphon has eaten the Mythical Gryphon Zoan, I'm not sure Shanks beat Loki in a 1v1.
Shanks isn't Luffy, Luffy admires Shanks. Shanks has no problem playing dirty to win. Shanks COULD beat Loki, but, the damage would be too severe, so, Shanks went the easier route.
I think Loki has two big weaknesses. One of them is known, the other is speculative.
Known Weakness: Seastone. This is Loki's largest weakness, by far, due to Loki's size; lot of area to hit. At the same time, like with the Salt Usopp shot in to Oars mouth in Thriller Bark, a few nails aren't going to be enough: if you want to stop Loki's power, not just his Fruit, you need a large amount of Seastone. Based on what we've seen with his "fight" vs Gunko, Loki has Future Sight. So, the biggest weakness Loki would have, is people who can counter-act his Future Sight, and snipe him with Seastone. More on this in a minute.
Speculative Weakness: Ragnir. I think Ragnir is totally loyal to Loki, since Ragnir was willing to strike Elbaph's Adam Tree, despite knowing what lightning hitting that tree would cause. Maybe there's another skill Loki has that made Ragnir comfortable, but, Ragnir's willingness to set Elbaph on fire for Loki makes me believe Ragnir is loyal to the one who eats Ragnir/is worthy. Ragnir won't betray Loki, BUT, Ragnir is an adorable woodland creature. Have you ever seen, how mindless Squirrels can be when they're zoned in on a nut?
So, this is how I think things went down.
I believe Shanks stopped Loki from attacking the Holy Land in a suicide mission, in Harald's honor/memory. So, I think Shanks fought Loki in one of 5 locations:
1. An island they agreed to duel on due to a challenge between one of them.
2. Elbaph itself (if this did happen, we will likely see scars of this battle)
3. Outside the Red Line (possible since it would allow Shanks to target Loki where he's weak, near water)
4. On top of the Red Line itself
5. In Shanks' territory after Loki invaded it (this I doubt, since Loki's focus seems to be 1000% on destroying the World Government, not gaining territory/allies. Loki is too prideful to want anyone but Elbaph warriors serving under him, which is why he's destined to lead the Galleira as Captain)
https://onepiece.fandom.com/wiki/Haki/Supreme_King_Haki#Observation_Killing
1. Shanks Cancels Loki's Future Sight.
Shanks is the first character introduced with this, and Loki is the 1st Top Tier outside of Luffy who has been shown using Future Sight. This makes me believe Shanks' Observation Cancelling was used here, as it would affect Loki badly, if he was fighting all of the Red Haired Pirates at once.
2. Lucky Roux Lures Ragnir Away With Food.
Loki has been shown to be a Glutton, and I imagine Ragnir, after being trapped in a storeroom for centuries, appreciates eating food. It's possible Ragnir just gets hit by Seastone, as I'm not sure who will be the the "Sniper" Here. At the least, I think Roux will distract Ragnir with food, as Chef's in One Piece have constantly been shown as using food to achieve victory, like Streussen and Sanji. Obviously, Sanji still needs to surpass Streussen, but that's another thread.
I wonder what Ragnir likes to eat? We know from Spandam's Elephant Funkfreed's favorite food being bananas (https://onepiece.fandom.com/wiki/Funkfreed#cite_note-15), that weapons that eat Zoans enjoy food, though Ragnir's survival for centuries without any known food source makes me believe that Zoan Weapons don't NEED to eat, they just enjoy it.
Also possible Roux lures in Ragnir with food, then cuffs him with Seastone, or grabs him and knocks him into the sea for asset denial. Either way, big focus here is getting Ragnir out of Loki's hands as fast as possible.
3. Yasopp and Beckman Blast Loki with Seastone.
Loki is a giant target, and, as fast and strong as he is (and he could be faster in Zoan forms), he is NOT avoiding Seastone fire from Yasopp and Beckmann, especially Yasopp, who, based off of Usopp's Observation Haki, is likely an Observation Top Tier. Beckman's firepower has been showcased via Kidd, and I would NOT want to get shot by this man. Loki isn't avoiding them both firing Seastone at once. As stated before, Loki will likely be able to resist smaller amounts of Seastone, while loosing the ability to use his Fruit. We know this, as even with one leg chained to the Adam Tree in Elbaph, and while half-dead, Loki was able to do this with Ragnir:
It will take a sizeable amount of Seastone Bullets to take Loki down.
Keep in mind I believe Gryphon is a Sword that ate the Gyphon Mythical Zoan, and can detach like Cerberus detached from Shamrock's Sword. Shamrock RETAINED HIS SWORD during this, meaning that if Gyphon ate this Mythical Zoan, Shanks could fight with the blade and the Zoan form at the same time.
In this scenario, excluding other Red Haired Pirates (I think Shanks brought his top Officers to the fight), we would have:
Shanks and Gryphon attacking Loki directly, while Beckman and Yasopp rain down Seastone fire, and Shanks Cancels Loki's Future Sight, is a legit loss for Loki, that makes everyone involved not take any real Ls. Shanks pulled up to Marineford and clashed evenly with Akainu, we've already seen his strength.
If Shanks/Loki fought in a legit 1v1, they'd destroy everything around them and someone is ending up like Aokiji at the end of it.
Since Shanks loved Harald and most likely is fond of Loki as a result (another Buggy situation, furthering my belief Loki will ally with Cross Guild and Buggy, Rocks' other son), Shanks didn't want Loki to kill himself attacking Imu, either of them to injure each other seriously, nor for their battle to destroy wherever they fought.
So?
Shanks outsmarted Loki, and Loki views him as a Coward for this.
Shanks and Loki are both legit top tiers, and should be treated as such. But, when it's revealed Shanks took this route, rather than do a 1v1, people are going to call him out. Still, once again, Shanks' goal here was never defeating Loki: it was keeping his friend Harald's son from dying a pointless death trying to get revenge against the monsters who killed Shanks' Mother and killed Loki's Father.
Gunko and Shamrock's defeat of Loki while he is gimped by Seastone foreshadows the fight with Shanks.
