After the TV series and the last few movies, the timeline is a piece of Swiss fucking cheese, but I think the plan as of T3 was that future events are inevitable. You can delay the future, but you cannot change it.
Multiverse or not, everything after "Terminator 2: Judgement Day" is exclusive to itself. The third and fourth movies simply do not consider the series, which ignores the movies. Both of those ignore the theme park ride (which includes content that Cameron himself has sanctioned).
It is less a question of it being Swiss cheese and more a question of it being several different blocks of cheese altogether.
Anyway, as for why two guys with the same name have to be the same guy? Well, it seems to be more of a thing in TFs than any other fiction I've encountered. I think the idea is that in any given universe there's generally only one bot with said name and that's that universe's version of that character.
Does not make sense though. Why should there ever only be one guy with a given name, especially when there has been precedent in G1 for different (albeit obscure) guys having the same name? That annoys me almost as much as "recolours are related".
Who'd have thunk two people would be named Dominic Gobbledygooker?
No joke, at one point, I started thinking of my screen name and my real name as two wholly different people. (Once, when talking to Honey Bear on the phone, I referred to "Dom" in the third person. And, that is when I started scaling back on the alias.)
In TF though, the multiverse was primarily put into place to explain how there could be content that clearly contradicted each other on a base level (Armada cartoon, Armada comic) and not have either version be "wrong."
I am old enough to remember the first time through with this. I never gave it much thought as a kid. I just knew that the comic was the comic, the cartoon was the cartoon and the back of the box was the back of the box. There would be some similarities. But, the character on the back of the box did not perfectly match the comics I read or the cartoons I watched. Sometimes, the characters would not even look the same. In the case of "GI Joe", the file cards matched the comics a little better (as they were written by the same guy. But, even then, I just accepted differences.
Even after seeing Marvel's "What if....?" and being exposed to the idea of a formalized multiverse, I did not immediately apply it to TF or Joe because I understood that there was no need to and that there was no intention by the creators to do so.
A few years later, the "GI Joe" trading cards created the first "mixed" setting for Joe, where elements of the cartoon and comic mixed. For example, Snake Eyes and Storm Shadow had their history and an unusual successful Cobra gunner managed to kill 7 Joes when he should have let them go. But, the Joes also fought and defeated Cobra-La. Oddities of this setting include the first and (for 15 years) only appearance of Crystal Ball (the only original character whose card was not written by Hama), and that was posthumous.
GI Joe tends to have its insular fandom swear up and down that only the original Marvel comic written by Larry Hama is "true canon" and literally any other interpretation of GI Joe is blasphemy. This includes the Sunbow cartoon, the early 2000s CGI cartoon films, Sigma Six, the films, IDW's stuff, and any continuation of the Marvel run not written by Hama.
You forgot the absolute hatred they have for Devil's Due Productions. In fairness to the Joe fandom, they seem to (as a whole) have learned their lesson in '09 after the property nearly went away completely (after the movie did far worse than a long-running property should have). But, it took them decades longer to learn that lesson (and accept new things) than it should have.
Straxus didn't take over a clone Megatron body. He took over actual Megatron and tried to trap Megatron's mind into his disembodied head. He failed and they both wound up in Megatron's body which is why Megs went insane. And Megatron returned because when he blew up the space bridge, it dropped him somewhere on Cybertron, rather than killing him like everyone thought and then later the Straxus thing happened.
Not quite.
On page:
Straxus made two attempts to take over Megatron's body. The first involved trying to take the original Megatron. When that failed, Straxus took a "cloned" Megatron (built around a nameless Decepticon). The "clone" (which Straxus programmed with Megatron's memories and personality for reasons that I do not even pretend to understand) was the Megatron that Furman used for several years, until just after "Time Wars" in the UK, when Megatron was returning in the US.
Off page:
Around the time that the US comic was preparing to write Megatron and Optimus out, Furman was trying to build a cast of "forgotten" characters that he could use as needed. His idea was that lesser used characters would be easier to use as he would not have to reconcile them to US content. (Remember, the US:UK balance was very one-sided. The Marvel UK had to play ball with the US, and had no say in what Marvel US did.)
Prime's death in the comic was decisive enough that Furman could not do anything about it. (Though, reading "Prey", I get the feeling that Furman was planning to "wait and see" if he could pull something off.) Megatron on the other hand was accessible, having a less clear death.
Furman used Megatron (along with Ravage and a few others) after their apparent deaths in the US comics. (Despite Furman's efforts to keep things in order, real breaks start to appear between between the US and UK series around issue 50 of the US comic. These breaks would continue more or less to the end of the series, likely being made worse by Furman having less time than he planned to introduce the Action Masters.)
The "clone" Megatron (revealed and disposed of in later black and white strips) allowed Furman to use the same Megatron for late run US and UK comics without having to worry about the baggage that the UK Megatron would have accrued over the course of the UK exclusive strips. In order to work, the "clone" needed to have Megatron's memories and believe that he was Megatron (I forget if Furman even contrived a reason for this on page). This also does not account for how Straxus transferred *his* mind (rather than a copy) to the "clone" body.
While the "clone Megatron" did not patch all of the breaks between the UK and US comics, and it causes a few problems, it was probably the best solution that Furman had available.