1. Apple. Apple provides a unique premium brand experience that is currently unmatched by most other's in the computer industry, although Sony comes close on it's consumer computing products. It's the same phenomenon that makes companies like Starbucks, BMW, Louis Vuitton, and other luxury brands successful in the face of better value competitors.
This is diminishing though, as there's enough issues now. The marketing slogan "It just works" isn't true any longer. Bugs in the OS (i.e. the thermal issues in the '09 MP's under Quicktime X code) have blown this statement. So has hardware, even in base models (i.e throttling of the ICH10R specific to '09 MP's as well). In some cases, hardware upgrades may only be possible via assistance from 3rd party vendors such as Maxupgrades or Trans Int'l (i.e. adapters of some sort), as Apple offers no solution at all.
2. OSX. ... The Mac Pro represents the most extensible powerful platform that legitimately runs OSX.
This is mostly preference, but in some cases, necessity, due to the software investment (especially for corporations, as they need a single point of contact for warranty/support).
Of course, any argument based simply on value, price or performance, will make a Mac Pro (or any Apple product for that matter) seem like a poor purchase decision.
It's the primary part of it though. There's other factors, such as software needs or necessity (already have the software, and it's not possible or practical to switch to another platform).
Then there's user experience/satisfaction <platform integration> (where I've the impression you're focusing on). That one was in OS X's favor in the past, but not so much now, as it's showing some issues, and MS has actually gotten their *** together. (They finally made a real effort to work with other companies to improve the user experience this time around, and it's paid off). Even die hard OS X users who frowned on (if not outright despised) past versions of windows have been surprised with their experimentation with Win7.
Now, back to the topic at hand... The fact is, given the 3.33GHz CPU is a $1200 premium over the entry level quad, their's not a lot of savings to be had for the DIY'er... which is unusual for Apple. However, the question remains, is the added 25% performance worth it? In my opinion, if this option were available last March when I purchased my 2.93Ghz for a $500 premium, it would have been a tough call to spend an extra $700 for the 3.33Ghz. I likely would have purchased the same system I have today.
You even placed value on the systems offered, and selected accordingly for your needs. Granted, it's within Apple's lineup of MP's, but from a hardware perspective, they're not really any different at all from other vendors (hardware; minor tweaks, and in appearance, which Apple does exceed at by many's idea of attractive). Dell's (and others) are quite functional, and have nice internals, but are fugly in terms of exteriors. Worst case, I'd be willing to hide it if it's the best solution for the task intended.
Who says they ever had it? They have what(?)... 5% of the computing market but reap 50% of the profits available? Arguably, they don't own any market segment but are ridiculously successful.
With computers NO, but they've been gaining market share. For the device market, IIRC they do with iPods, and have made major inroads with the smart phone market (iPhone = Yes here as well, if you limit it to comparison to say any particular smart phone company), according to MR's front page articles recently.
As with Dells, I'm pretty sure that's just a comparison, but nonetheless that $1200 is a lot of money; for the price difference I could buy a faster video card, HDD/SSD, etc.; that's substantial.
It was, as you can't get a 100% spec by spec comparison. Different parts in terms of HDD size, graphics cards, and PSU rating,... used in the base model. I got close though, as it had the same CPU and memory (type, capacity). I even added in a 1394 card.
But $1200 isn't minor. Maybe $200 - 300 given the parts parity (essentially a base system beyond CPU and memory), as there's not a drastic improvement in support or warranty to make more worthy. But certainly not more than 4x that.
And not many folks like paying a "premium"; if you say you do, it's pretty much asking to be ripped off. If you can have two of the same machines in every way, would pay more for one that says "Special Edition" and nothing more?
Marketing does just that. They create an aura of elitism around a product that aside from appearance, is essentially identical (if it isn't actually the same exact circuits) and charge more for it. Maybe an additional feature or two is added (system engineered line of offerings, that differ by small amounts in terms of parts and cost).
They've learned people will pay more for the same/similar pile of junk they sell otherwise. Got to love ODM suppliers. A few products (say 3; base, mid and high feature set), 50 different enclosures and brand names...
I'm also intimately familiar with ///M.

As you probably know there are definitely competitors out there that offer 400+HP products (some at lower price points) but that doesn't change our enthusiast mind-set one bit... does it? Same for the lady (say, for example, my girlfriend

) who swears a Louis Vuitton hand bag is better than the knock-off for 1/10th the price.
Not the best comparison with automobiles, as they've technical differences. It's not the same exact engine, transmission, brakes,... sold under a different name. There's different engineering and manufacturing involved (even if parts are sourced from the same suppliers. Take BMW and VW for example, ordering springs from Eibach - they're not going to have the same specifications for competing cars, as the suspension design isn't identical.
The hand bags either, as IIRC, Louis Vuitton is handmade with much higher quality materials (quantifiable), while the knock offs are machine made in China with sub-par materials.
In the instance of the computers, the main features and parts used are the same. Intel chips, and the boards are based off of Intel's reference design, so the features are essentially the same (differences like 1394 on the board, which would likely require a card in another vendor's system, and perhaps different chip vendors for NIC's and Audio). Other options as well, such as built-in RAID, additional SATA or SAS chips can differentiate boards, but the primary systems are the same.