It's happening again.
Are we back to early 2015.
To actually talk about the points.
Bayonetta's CQC is better than Link's. Yes, Bayo's jab is stupidly slow, it's frame 9, f-tilt is frame 12 but covers a good range and can be surprisingly safe on shield. Bayo however has a frame 7 d-tilt which when spaced out can be safe and start combos, other than that she has up-tilt which is frame 7 but isn't as safe on shield so it's more of a commitment. Link on the other hand has mostly jab, frame 7. It's not a terrible fight for Link, but Bayo having more options gives a plus to Bayonetta, and with Bayonetta a hit leads to more combos, due to having string starts from f-tilt, d-tilt and up-tilt.
Another thing, Link can't hit Bayo's shield because a lot of things that 'look safe' aren't safe to Bayo's frame 5 OoS WT punish. This makes hitting buttons scarier for Link than it is for Bayo, because Link's best OoS option is a frame 9 up-b and is super committal, while witch twist...isn't.
One thing you never brought up is how Link deals with Bayo's b-air and ABK down pokes on shield. Link's bad JS, air speed and frame data in general means that Link can't really punish things, esp the bounce back on ABK on shield. You need a very long-reaching aerial, and Link's frame 21 OoS F-Air won't be fast enough as ABK has ~20 frames of end lag.
You never really bring up Bayo's other options for edgeguarding, things like drop zone Witch Time, or drop zone N-Air. Both of these options will punish you for trying to tether, and will force you to recover high, which can then be D-smashed/d-aired or just n-aired over and over again. Link with his slow high FAF aerials outside of n-air will be hard pressed to stop Bayo when Bayo is just n-airing over and over again since it lingers for a long time, has a big hitbox and sends you at a very bad angle for bad recovery characters.
I can see where Link deals with Bayo's recovery, but I think Bayo will still win off-stage as Bayo has much safer options for dealing with Link's average at best recovery. Bayo on advantage is, well, Bayo. It's rather ridiculous. Link's slow movement means he'll be harder pressed to punish Bayo's mistakes compared to say ZSS.
tl;dr
There's no way Link beats Bayo 6-4 and I'm very surprised you ever said such a thing.
Okay, I can understand that you're surprised about this, but again, I am going to stand strong on my thought that the MU is 6-4 Link's advantage, and I'm going to address your points, though at the time, I should have made my points on some of these:
1) I can understand that some of these things can be turned around, and yes, Bayonetta does have a really great CQC that can cause her to have a great advantage state. Her Frame 7 D-Tilt is a really great option when spaced, which I agree, it's good for hitting my Link off guard. But while you do say Bayonetta has more options, she has a lot more options up close, a sort of "in your face" one. I can conversely say that Link has it better at middle range or near the tip of his attacks, as he does have attacks that can have their set of distance. Jab and Down Smash come to mind, but Down Tilt is also a safe option at middle range CQC. Both Link and Bayonetta have their fair share of good CQC, but they have their own different high points. When Link's at a longer range than Bayonetta, he comes off as harder to punish the longer he's away during it.
2) I do agree, Link does have a lot of unsafe things about his attacks that Bayonetta can take advantage of. Link definitely has a punishable OoS that, especially considering it can activate a counter, is super situational. However, in terms of countering Witch Twist, I'd probably attempt using a legitimately safe Down Tilt due to its low recovery time needed and the range you have with it.
3a) I should have brought this up, too. For Bayonetta's B-Air, I would at least attempt to punish it with a fast enough tilt, smash or even Link's Jab or Bombs (given I can have Bombs). If I can be honest, I'd try spot-dodging Back Aerial to punish it.
3b) As for Afterburner Kick, bouncing from a shielded Link is definitely powerful and using F-Air is a bad option OoS. I do wish Link did have a better JS, though there still are options Link can have that don't just have to be aerials. I advocate that Bombs could be a good method, or a Recoil Special Boomerang (make Link go backwards when throwing the Gale Boomerang). That way you can either gain distance or punish in a better method.
4) Drop Zone Witch Time is something I've never seen my opponents really do, but I've definitely been punished more times than not with the latter, Drop Zone N-Air. It's definitely a challenge for me to go against, so I'd attempt to get behind it so that way I can be hit towards the stage. Of course, that's also risky since I'm susceptible to stage spikes. But let me ask, how the heck can Witch Time punish me for trying to tether? Aren't tether grabs that latch to the ledge hitbox-less? So wouldn't Witch Time be kind of redundant? Or even punishable?
5) I agree, Link definitely would find it harder to punish Bayonetta's mistakes, but when Bayonetta makes a big mistake (preemptive Smash, Witch Time or laggy attack), Link can take sole advantage of that and has moves that will punish her heavily. It's more of a patience game than just ZSS's moveset.
And Bayonetta does have things like the F-Air string and some very insane and fast combos. I've seen these on videos and I've experienced combos first hand, but still, I think due to Link's ability to shut down some things she has can make the MU much more easy. My replies might not be strong, they might even be weak, but that's okay, I'm just here to learn right?
TL;DR
We can debate this until we both come into a sort of harmonic place together.