I agree that The Man Marked By Flames is probably a member of Roger's old crew. But, I can't believe you skipped over the biggest, most important crewmember of all!
Personally, I'm betting on The Man Marked By Flames being...the Oro Jackson itself!
Specifically, the klabautermann of the Oro Jackson.
For one thing, we really haven't done anything with klabautermann at all since Enies Lobby. If they're going to be important to the story, we need them to come back into it ASAP. Otherwise, the Merry's sacrifice is a touching, but kind of odd, tangent to the story.
Second, if it was the spirit of the Oro Jackson, then it might have the Egg or whatever hatched from it, along with it as a travelling buddy. We get to solve two mysteries in one.
Third. we still have no idea what happened to the Oro Jackson. One of the most famous ships in the entire world and we have no idea what happened to it. Not even a offhand mention of the Marines sinking it or something. It just disappears from the story.
Fourth, the Oro Jackson most likely would have formed a klabautermann. We know not all ships get one, only ones that are especially cared for. And Roger and his crew seem like the type of people who would have cared for their ship enough to get a klabautermann.
Fifth, the Oro Jackson went everywhere that Roger did. Therefore, it would know the location of all the Poneglyphs, and thusly could take one in order to protect it. Maybe the Oro Jackson wanted to make sure that no one "unworthy" got to Laugh Tale and wanted to protect the place for his former master. Maybe whatever hatched from the Egg helped load the Poneglyph onto itself. It's a little awkward, but this is One Piece, so it's possible.
Sixth, if the Oro Jackson has been sailing around as a "ghost-ship" this entire time, it would actually make sense if it had a bunch of battle-damage from various fights. Plus, if the Egg turned out to be a Dragon or something then maybe it burned the ship? And it would no longer have a crew that could repair it, so it would just keep getting worse. And that battle-damage could be reflected as "scars" on the Klabautermann's body. We really don't know how that works.
Seventh, a klabautermann could, in theory, keep sailing around the seas without having to ever stop, like The Man Marked By Flames is said to do. They don't seem to need to eat or rest. So, the Oro Jackson would never need to anchor at any port, in order to resupply or feed themselves. They could sail non-stop without much in the way of problem.
I just think it'd be neat. I can't say for certain that's the way Oda's going to go. But, I do think it's possible.
