I didn't go into more detail because there seems to be a limit on characters but I would have done the first quest during 1.0 because I remember having the chocobo as a mount at that time with the Immortal Flames but when I came back there is no whistle on inventory neither does it show on Calamity Salvager NPC.

The Feisty chocobo quest doesn't show as available, the little chocobo doesn't show at all which leads me to believe the game considers it as done already.

the only reason that I can see for this is that at the moment I'm with The Maelstorm but it still should be possible for me to obtain a companion.