Toon Link's presence stretches across the horizontal length of the stage. He can throw rang while moving, and at several distinct angles that cover space well. It'll clank with shadow ball until it's almost fully charged. His bomb will always hit and nullify shadow ball, even fully charged. Tink's punishes on Mewtwo are objectively stronger than ours on him. He has a very good tool in aerial up-B to kill, he has lots of moves that put floaties into that position to get sweetspotted by up-B, and he has solid combo starters.
Going down your list:
If bomb pull is about 40 frames let's math out the reaction time for a raw teleport punish, assuming the Mewtwo is at the correct spacing and Tink isn't moving whatsoever, so there won't have to be mental calculations that could slow reaction time.
40 frames for pull start. At average human reaction time Mewtwo begins jumpsquat. That average reaction time is 15 frames for a visual stimulus so let's go with that. Jumpsquat is about 5 frames, let's assume 20 frames before y position != 0. Assuming your numbers are correct, teleport takes 17 frames to travel.
That means, assuming average reaction time in a game with as many options as Smash, we can close the distance in 37 frames. Fair will hit on frame 43. I'm not sold on the concept that we can consistently react to that without hindering our ability to play neutral. Also keep in mind the reaction time assumes we're reacting to the first frame of bomb pull, which doesn't have significant visual cue. Punishing bomb pull consistently on reaction seems to require either consistent 12-frame reactions to bomb pull, enhanced reactions by actively looking for bomb pull, or a read on his bomb pull. This is all without considering the possibility of Tink's movement while pulling the bomb or the misspacing that would result in Mewtwo hitting the bomb and exploding it.
Let's say boomerang has 45 frames of startup before the projectile leaves Tink's hand. Using our math from the above point we can get fair out on frame 43. Most of my bomb comments apply here as well. If we don't react quickly enough or we lose a few frames in execution we get hit by point blank boomerang. That's double-digits % and a huge combo opener for Toon Link. The boomerang also doesn't have a notable startup on frame 1, so we're likely not reacting for at least a few frames anyway.
Mewtwo's ground game has to be more intentional than Toon Link's. It's on us to stay in a range where Toon Link doesn't feel safe about using his projectiles. He has faster ground speed, faster air speed, and better range on his aerials (sans back air). We have more range on our grounded moves. Movement is such an important part of a ground game and Tink beats us in the air and on the ground there. His moves are quick and low-risk with good spacing. We have to commit more to get our advantage of range because our moves are slower, grounded moves are almost always slower than SHFL aerials. This is more of a disagreement than a math problem like the above two points, so if you believe that Mewtwo can hold his own against Tink in the ground game don't let me convince you otherwise.
If Tink throws a boomerang and we reflect it he has the time to pull a bomb. If Tink throws a bomb and we reflect it he has the time to throw a boomerang. While not negative for us, this doesn't really fix the problem of Tink having a projectile either onscreen or in his hand.
Also, minor gripe, you say this above and I have a few issues with it.
"Bomb toss isn't the optimal punish because of trade risk and resource consumption if he misses the read. [snipped]On top of that if m2 reads an aerial at low percent m2 can teleport into cc and punish."
Bomb toss is a strong punish and still good on trade. On a clean hit it can lead into many strong moves for either combos or kills such as any aerial, forward smash, aerial up-B. Even on trade Tink can often get something out of it, since he's liable to take less of the hits than the object he's throwing it at once it leaves his hand. Due to his ability to maneuver while pulling a bomb resource consumption isn't an issue unless he has very little stage control. If you're suggesting an autocancel teleport into crouch cancel with the second statement, then I disagree with you on the speed of Tink's aerials. SHFL aerials on Tink are not slow, his fastfall speed is respectable enough to whiff aerials to dissuade teleports and still be able to play a ground game.
Also, your statement that nobody can react to teleport is wrong. I play Mojo's Fox every week or so, and have been for over a year. When he focuses his neutral on reacting to teleport he will up smash me out of teleport every time. Up smash has 6 or 7 frames of startup, and he'll consistently hit me before nair will start. I have to play the ground game, which involves moving out of the effective range for teleport, before he'll stop looking for it. They're assisted reactions, yes, but Mewtwo's other options at that range don't require an immediate response so the mental capacity used to react isn't a huge liability if no teleport comes.