I found that Miraidon/Koraidon is embedded in the BoxInfo Block Data [0D66012C] when you can't put him in your party yet.
Essentially what I did was:
Open your Scarlet Save File in PKHeX. (Change Trainer Info to Pokemon Violet, and your Koraidon Pokeball to Miraidon Pokeball, if you haven't yet.)
Under SAV tab, save your Scarlet Box Data first with "Save Box Data++".
Within the same save file, Click Block Data, Navigate to "*Object BoxInfo" in Block Key.
Click "Import Current Block" and find a [0D66012C.bin]* Pokemon Violet Box Data where Miraidon is embedded. (I recommend to make your own to match Trainer ID and SID* but you can use attached.)
Close the current window. File > Export SAV to a separate location and File > Open it again to update the data displayed
Drag in the Box Data file you saved from step 2
Now File > Export SAV it again and put it on Violet
* Create a Violet Save file changing to same Trainer ID and SID at start before Miraidon Encounter then once you get him at Lighthouse, save, open Violet Save in PKHeX, navigate to step 3, Find "Export Current Block". (Probably necessary to make him obey you once you first use him in battle.)
Still playing this save file for a while. All gyms, titans and team star are still marked the same way I finished them. I'm not still 100% with the game so I'll write back if I have problems (will probably check his Trainer ID once I get him in my party). But I'm kinda sure that event flags are kind of the same between this two versions from the only slight version differences reported on the internet though.
Hopefully, PKHeX updates the program to also change this kind of thing.
UPDATE: You won't probably have to do this anymore because you would also need to change Trainer Data of the Ride Pokemon. Check next post..
0D66012C.bin