According to SHQ news, Sonic Mega Collection has the feature for playing as Knuckles in Sonic 1, 2, and 3(like the S&K lock on feature). But the original idea for playing as Knuckles in Sonic 1 was scrapped years ago when S&K was about to be released, due to a minor bug in the gameplay which froze the game. If this is so, can you really play as Knuckles in Sonic 1? Gracias.
As far as I know it's like Sonic Jam, so the games are untouched. You can set S&K to play the Special Stage minigames for Sonic 1.

~ SA Tails