I know but it has thunder in the name of the technique. i know it doesnt teleport at the speed of thunder im just stating a real life fact.
You're kind of contradicting yourself. You said you aren't taking the name Flying Thunder God literally, and then you claim that lightning is faster than Thunder.
Anyway, these are the facts:
Yondaime's FTG Technique is a space-time technique, and therefore is instantaneous.
Lightning Release technique are known to move slower than natural lightning, so much slower that you can visually track the lightning as it moves with your naked eye. So ordinary lightning release technique's speed would pale in comparison to the FTG technique.
If you want to talk about natural lightning, or Kirin, than it is much harder to tell but I still think the FTG wins since a lightning strike is very fast but not instantaneous.
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Long story short, don't take the name so literally-It's an instantaneous teleportation jutsu.