Where to begin...
First of all the FirePro W9000s are $3,000+ each, not combined, but they will surely not be the only graphics choice as many power users do not need graphics performance. Secondly "FirePro" is branding for better support, better - optimized - drivers and ECC video RAM. They have such a high price as add in cards in the PC world because it is a small market using them for efficiency in business and research i.e. those prices are not extreme to the audience they are intended for. Hardware performance wise the W9000 is similar to a Radeon 7970 as they share the same GPU.
Apple are placing a custom order for several hundred thousand graphics processors and I doubt they will be paying more than $800 to AMD per system with dual W9000s and I would expect a base model to have dual W5000s as many users of these systems don't need graphics performance which would likely cost Apple no more than $300 per system.
CPU wise the logical choices would be:
Xeon E5-1620 V2: 3.7GHz, 4-cores and ~$300
Xeon E5-1650 V2: 3.4GHz, 6-cores and ~$550
Xeon E5-2697 V2: 2.7GHz, 12-cores - I was able to find a pre-order for $2,299 by searching with the box code bx80635e52697v2, but we will have to wait to see what Intel are pricing this at. $2,500 upgrade from Apple could well be on the cards - maybe even $3,000.
None of the 8-core E5-2600 V2 Xeons make any sense on their own because of their prices, maybe a 10-core but again not great value.
The 128GB SSD isn't an off the shelf part for a tiny niche market. It is a design going in to hundreds of thousands of units; it won't add a huge amount to Apple's costs compared to if they were using an off the shelf 2.5" SSD. RAM is probably $4-$5 per GB for Apple and a 4-core system would likely start with 8GB.
So Xeon and FirePro do not mean high starting costs. Apple could have a box for $1,999 if they wanted to really be aggressive. Sure prices on the high end will be steep, but how steep will depend on how Apple price their graphics choices like the PC workstation market or more akin to the consumer cards they are as powerful as.
Yes, Xeon and FirePro do mean higher starting costs.
XEON E5 Family
The Xeon also is a choice of very few options in this new Xeon list by Intel.
We know its E5 based from Apple and configurations up to 12 cores. Either a 6 core or 12 core option. There are no longer dual sockets. It's a single socket board.
http://www.chiploco.com/intel-xeon-e5-2697-v2-benchmarks-and-price-leaked-28077/
Xeon E5-2630L V2 6 Core 2.4Ghz is $701.01
Xeon E5-2650 V2 8 core 2.6Ghz is $1335.85
Xeon E5-2643 V2 6 core 3.5Ghz Pricing is N/A
Xeon E5-2695 V2 is a 12 core 2.4GHz model that matches Apple's latest 12 core set up and it is $2675.39.
Apple has never offered so many CPU choices. There are only 2 12 core options.
One at $2675.39 and the other at $2949.69.
This means it isn't targeted for folks who want a tower on an iMac budget, even more dramatically so than the prior Mac Pro.
Now with an agreement to purchase say 100k of these Apple can move the price point down, but nowhere near the levels you hope like they could with the iMac.
FIREPRO
Dual GPU standard.
The 4096 Shaders mentioned in the Keynote, while mentioning each GPGPU can hold up to 6GB GDDR5 means up to 12GB GDDR5 solution.
More to the point, the FirePro dual set up is a unique design to Apple.
They are GCN 2.0 based cards either using the upcoming 20nm/14nm FinFET or the last run of the 28nm line. Their PCI-E 3.0 interfaces are unique to Apple's model. They aren't going to be built for any other brand or OEM.
Apple can reduce the cost by investing into the co-development of the new designs to meet their new Core design and most certainly they have done so.
Yet, either way you shake it, this WORKSTATION isn't starting at $1999.
They emphatically stated up to 12-core, dual FirePros producing 4096 shader cores.
The FirePro W10000 provides 4096 shader streaming cores at 6GB GDDR5
The FirePro W9000 provides 2048 shader streaming cores at 6GB GDDR5
It is a reasonable assumption that this new design is a dual W9000 level GPGPU design for up to 12GB GDDR5.
This system will be unique to Apple and that adds in cost. Apple can absorb some of that cost by sharing the development [and has done so], but not to levels where you think you're getting the baseline at $1999 or even $2999.