This is why certain updates for the iPod Touch cost money while they are free for iPhones: It is entirely driven by how Apple writes up iPod Touch vs. iPhone revenue.
"Apple has for the first time made this full iOS upgrade free to all of its iPod touch customers, rather than charging the customary $10 fee that provoked groans in the past."
(http://www.ilounge.com/index.php/reviews/entry/apple-ios-4.0...)
This leads me to believe that the whole accounting rules canard was just a way to make more money. Why did they start charging for XCode? Because you'll pay it.
That being said, they haven't said that the XCode charge is a subscription accounting thing, so there's certainly no logical reason why you may not be correct in saying that they are charging for XCode because they can. I'm guessing otherwise, but this is armchair speculation.
UPDATE: I was wrong about subscription-based accounting affecting how Apple accounts for expenses. Here's a link I found:
http://www.macrumors.com/2009/09/23/standards-board-approves...
Or Apple's accountants changed. They seem to be very strange people, and I say that in a bad way.
> And in any case, if that were really true, why not charge a penny? Or the download cost? I don't buy it.
If they think they need to charge for Xcode 4, they probably think amounts under that would be seen as non-compliant. Facetime was $.99 and shipped with new macs.
The law is not particularly concerned with whether the major version number or the minor version number changed. It's all about what features changed.
Apple reports iPhone revenues over a 24 month period, this is called subscription accounting. Since an iPhone is sold as a subscription, Apple can write off services associated with providing that subscription on an ongoing basis, i.e. give all upgrades away for free.
http://tech.fortune.cnn.com/tag/subscription-accounting/
iPod Touch and Mac revenues do not use subscription accounting, therefore Apple is not allowed to give away major OS upgrades for these products, it must treat upgrades as separate products that make or lose money for themselves. Apple is not allowed to give away a major iPod Touch upgrade and apply the costs of writing the upgrade to its iPod Touch business.
I am certain of the rules around subscription accounting and its effect on requiring Apple to charge for iPod Touch and Mac OS upgrades (and Apple is happy to charge for OS X upgrades any ways).
Whether the $4.99 for XCode is a byproduct of these rules is conjecture. I think so, but I've looked all over and I can find neither my Apple Employee badge nor my Chartered Accountant diploma, so it's more than fair to doubt me on this.
p.s. Another clue to the reasons for the charge is contained in the fact that XCode is still free for ADC developers. Since ADC revenue is subscription-based, Apple can give away whatever it wants to ADC subscribers.