I don't know one way or another about the player's in-game agility, but the short shuttle and 3 cone have nothing to do with actually playing football.
They don't. They do have to do with him being agile though. If you look at Gaines draft write ups they almost all include words to the effect of "Gaines is an athletic and agile offensive lineman who will excel in a zone running scheme" (this was taken from an actual profile).
I'm not sure there is any such thing as separate in game agility, is not like you just turn it off for a game but turn it on for the combine. But either way his tape his full of his athleticism and agility. What it isn't full of is sound technique. His feet are fine, his hands are not. But that's why he's in the 4th round.