Well, I was always under the assumption that although the events with Luffy and Shiki in the Movie were non canon, the prelude to that fighting Roger during Ed War and getting that Wheel stuck in his head are canon. I know it would make it too obvious If Oda drew that man sitting there with Crocus with a feature like that, he could easily hide it or maybe somebody managed to get it removed.
Why would Crocus be all friendly with him? Someone he knows a former Crew Member would fit more. But as always for the benefit of the doubt, if it is Shiki, Oda would be able to give us a Story why they seem cool with each other.
Imo, its just Scopper full stop. One thing Ive learned recently is that with One Piece, Occam's Razor tends to be the way to go on theories. The most recent example that comes to mind it Kuma's reasoning for losing his mind. Many of us (including myself) thought there was some bigger reason for why he did it, but it was a simple as he wanted to save Bonney (we just didnt know she was sick).
Another example was my theories on God Valley. I had this whole thread and everything supporting the idea that the island was actually the flying weapon Uranus for a myriad of reasons. It could still be true, but unlikely now since Oda didnt allude to God Valley being anything special, just an island that was victim to the CD Rabbit Hunt. We also know Rocks went to God Valley because the CDs stole something from Beehive, thereby further supporting that the island wasnt special.
Finally, same reason I entirely believe now that the Burned Scar Man is just the former Shichibukai Ace defeated and not some ultra-super-mega Rocks clone villain that'll serve as Elbaf's big threat Lol
Tldr: it usually aint that deep with One Piece.