Let me start with a general statement, and then I'll get to some specifics.
When I started the MCP twenty years ago, I was determined that it would faithfully reflect the chronologies laid out in the Official Index. I wanted to use the Index as a skeleton, over which I could lay all the other stories that got left out of the Index. There are plenty of cases where we can read a story and say to ourselves, "Well, gee, it reads better, if it were this way." But I had to grant that Marvel was a better authority on the order of their stories than I was.
Now, of course, the Index was written by humans, and as such, they can make mistakes. But we have to show why the Index--or for that matter, the current listings in the MCP, whether they're confirmed by the Index or not--CAN'T be right. Just saying, "I like my way better" is a perfectly valid reason for changing things in your personal chronologies, but that's not enough to change things here. And that's been the policy, from the beginning. I apply it to myself, and we apply it to everyone else.
Now let's get to some specifics.
AlexEvangeli wrote:[In Carrion, MJ calls] her Betty Leeds in a derisive way because she is still married and dating Peter
Well, let's look at it. MJ bumps into Betty on the street and says, "Oh--Excuse me! Why--Betty Leeds! What are you doing here?"
Is this in a derisive way? I dunno. That's exactly what I'd expect her to say, if she bumped into Betty on the street, without any derision.
[In ASM 188, MJ] calls her Mrs. Leeds derisively seemingly again
Ehhh, I don't know about "derisively," but I'll grant your point here, because Marvel went to the trouble of bolding the word MRS. She's not attempting to make fun of Betty, she's just making the pointed comment that Betty is still married. I'm just not sure that either of these instances have any bearing on when MJ discovered Betty's status. Betty IS still married at this point, so her name IS Mrs. Leeds, and Betty Leeds. Since MJ's right in both cases, I don't think it serves to clear up anything about the timing.
Later on [in the Carrion arc] they part company peacefully, having talked and it very plain and obvious that MJ is aware by that point that Betty and Ned had split up, with Betty mentioning how she was immature to have jumped into that.
The plain and obvious is an inference on your part. Betty is saying she was immature to jump at the security of marrying Ned. This can be interpreted as, "I regret marrying Ned so soon." Someone could say that, even if they weren't separated, so I'm not sure you can assume that MJ knows about the separation from that statement.
In ASM 188, Betty says, "Mary Jane, did you hear about Ned and me?" MJ says, "No. Tell me."
To me, it seems that the creators showed us two scenes in two different books where MJ appears
to learn for the first time that Betty and Ned are separated, and the editor didn't catch the snafu. So we're left to determine which came first. We see in dialog that MJ doesn't know in ASM 188, and Betty doesn't know that MJ knows (because she asks). It seems to me that the better evidence suggests that MJ discovers in ASM 188, rather than the implied discovery in PPSSM.
So to answer the question from your original post:
[ASM 188] is according to the chronology placed after ... the Carrion arc in Spec (beginning in Spec #25) wherein MJ was made aware of Betty's seperation.
Why was ASM #188 placed after these stories?
My answer would be "MJ was not made aware of Betty's separation in ~ PPSSM 25. She was made aware of it later, in ASM 188." Now I realize that you could STILL make the argument that if MJ does discover Betty's status in ASM 188, then it re-enforces the argument that ASM 188 occurs before their "reconciliation" in PPSSM, but I can see both sides of it, and so it doesn't elevate to an error. We can't say definitively that the Index is wrong.
Now as to the placement of M/TU:
Your argument here appears to hinge on MJ's regret in ~ PPSSM 25 at the way she's treated Peter, in a previous issue of PPSSM, and yet has had interactions with Peter in M/TU in between these two events.
I know in my lifetime, I've said something to someone that I've regretted, and later had interactions in social situations with that someone and things appeared to be okay, but the things I said, and the regret that I felt, was still eating me up (but secretly). Eventually, I couldn't handle it anymore. I couldn't pretend that it never happened. Morally, I had to go back to that person, and clear the air, and apologize. Life works like that, sometimes.
So this ordering of events doesn't bother me. It actually makes it all seem more real to me.
But that's just me.