It's been mentioned several times that the Lineage Factor modifications that Judge performed on his children include only the Exo, Regeneration and Super Strength without the other Super abilities alluded to once being included on that list.
Going by how Queen showed to wield the list of Vinsmoke superpowers of Invisibilty, Poison, Sparks, Electricity and Gear Hands, they are most definetly Cyborg enhacements.
I guess the Vinsmoke siblings got these cyborg enhancements from Judge after they reached the appropriete age for surgery way after Sanji left as they didn't manifest these abilities back when they were still children. Besides Sanji not showing the capability to turn invisible -not talking about his speed here- even after awakening his Lineage Factor modifications is another evidence to these powers actually being mechanical in nature.
As for the origin for Sanji's Flames, I believe they come from his soul somehow as we know soul power is a thing in One Piece, plus iirc Oda did say that Sanji's soul burn hotter than any fire that's why he doesn't get burned. Either that or the Vinsmoke Clan or posssibly Sora's drug have some links to the Lunarians and somehow that resulted in Sanji being able to turn himself on fire, who knows.