That it was shiny was gone over fairly extensively in the game. As, in the games, Pokémon are basically the enemy (whether or not your starter was rare), it is perhaps worth considering that rather than it being in question whether this Gyarados was to be captured, as a shiny, it was also worth noting that it was probably meant to be first and foremost a difficult or formidable opponent in some sense, before any further process. The centering of it around moves like Thrash, etc., rather than having something which isn't supposed to battle you or not significantly, seems to support this. As such, if you were to catch it this might allow, if this side of things were by then permitted to show, for using the logic of the game as it were against it. There was also the possibly interesting call-back to Red and Blue, as well as to Red as the 'final' spectre of the game, making this 'Gyarados' something of a perennial rival in a way you suppose fitting the name.