The reasons are practical. IE is a nontrivial component

So - only trivial 'components' are permissible to replace.

And - who judges? Microsoft's legal and marketing departments, no? After all, MS declared that IE was integrated before MS developers smeared it across so many .dlls and forced explorer to depend on it.
you've probably never done hard time trying to get a nontrivial Java product to work correctly under several different vendors' JVMs

I've run ide's across different jvms (and platforms) with little or no problems - does the definition of 'nontrivial' mean that it didn't work when you tried it?
risk that neither Microsoft nor any other software developer in the same situation has any reason to take. And I believe it is unfair and unreasonable to require them to take it. Your thoughts?

Require? Funny, nobody asked MS to replace it's own product with competing ones (unless as a punishment for breaking the law as egregiously as they have been shown to).

This is not the same thing as allowing OEM's to customize products that they pay for.

More -
who do you think the user will blame? Whose brand do you think the user will lose confidence in?

Hmmm. Let's see. Let's say a Compaq product has a problem, and user A can't run his programs. He calls Compaq for support, and still can't get his stuff to run. Then he calls MS for support, and MS has him reload Windows (not far-fetched, it's a common enough response from MS). Suddenly, his 'pure' MS system runs!

In this scenario, we are to believe that User A will blame Microsft, not Compaq?

Let's try this - neither MS support OR Compaq can get things to run... The user will of course ignore the brand name on the desktop in front of him as the cause, as well, right? Of course they wouldn't curse 'that Compaq piece of sh*t'.

Now, let's look at Compaq support fixing the problem. Yeah, they might blame Windows. Do you think they won't blame Windows now?

OK - now the case that a value-add from Compaq increases performance or makes the interface more appealing - this is bad for MS how? Only bad if they DON'T actually have the best product, and can't compete on quality with the OEM's value-add.

Bottom line: Right now, the OEMs bear the responsibility for support, anyway. Saying that allowing OEMs to customize systems in any way that they want is 'bad' is denying that OEM value-adds bear importance to OEM sales. Even if the OEMs botched the job, that would simply make a 'pure' Microsoft system a selling point.
How many automobile manufacturers give dealers the freedom to modify cars any which way? Don't you think there are valid reasons for that?

If I buy a car and modify it extensively, then sell it - no problem. It's been modified, the 'stock' auto mfg. is no longer required to 'support' it (though I'm required to, and may offer an extended service plan if I wish) - and has nothing more to do with it. If I do this with 50, a hundred, a thousand a day, it doesn't matter. The auto manufacturers can't stop me. If I were to do this with Microsoft products, I'd be put out of business.

Your arguments seem to be a tired rehash of the MS-apologian practice of blaming 'third party' software for every quirk and instability that end-users experience (often without investigating the problem thoroughly).