can you be anymore specific with the details? which card was acquired? was it during the Hot & Cold mini game digging it up or was it from a chocograph chest on the world map? Was it bought from Mene with 1800 points? What color was his chocobo? Which cutscene froze?

You don't get the boat until disc 3, so by what you've said he certainly wouldn't have skipped from disc 1 to 3, if the skip happened after he got the boat.

It might help to clarify which airship you're talking about. If there's any truth to this, there's a chance the game recognises every vehicle on the world map the same, since as far as I remember you only ever have access to one vehicle at a time (separately from chocobos), so maybe it can be perceived as a sort of "vehicle level".

You say the airship was next to him after inserting the new disc, but none of the discs start on the world map (all of them start in cutscenes) so I'm pretty sure this would have nothing to do with the card but more likely putting in the wrong disc at the wrong time.

Probably worth mentioning though if this is the case, that it's sort of an unwritten rule across all speedruns to not really touch the hardware while the game is running, in FF9 this means not opening the disc tray to skip cutscenes, for example. In multi-disc speedruns, it's a rule to only open the disc tray when the game prompts you to, and as a result, skipping between discs like this may simply be impossible under the current rules, unless the game is still able to run through the story and FMVs while on the wrong disc (i.e. playing through disc 3 while on disc 1, then putting in disc 4 when you get to the end of disc 3).

Finally, the gold Chocobo bug is an old myth that has no proof of ever existing and, in speedrunning at least, is pretty strongly believed to not exist and is meme'd on a bit.

Hope some of this helps. If there's any truth to this, my speculation is that you've put in the wrong disc while standing in an unusual area or something. It'd make sense to me at least if he was trying the other discs because the correct disc kept freezing on a cutscene (due to a scratch). Maybe when trying the other discs the vehicle got a free upgrade

In your last post you said you didn't know the colour of the Chocobo...