It isn't free to have internal drives but the "marginal cost" is ridiculously cheap.
It is cheap primarily because it is included in the chipset. This C600 chipset used with the Xeon E5 v2 is non optimal for the Mac Pro 2013 design. However, this is probably the core basic design for the next 5-6 years.
A next generation Intel Chipset offering that swapped SATA functionality for:
Thunderbolt ( not as likely do to physical port placement distance constraints )
10GbE ( this is already a discrete Intel chip so quite possible )
USB 3.0++ Ultra-Super-Duper Speed ( or whatever USB calls their 10Gb/s upgrade
https://forums.macrumors.com/threads/1521001/ )
Is actually going to lower the cost of adding those two the Mac Pro. It would be a swap more so than the net push the current set up is.
With external options You have to have an additional power supply, additional case, and with TB, an additional controller. It is clearly more efficient to have a reasonable on-motherboard and in-case capacity for SATA expansion + PCIe (and maybe TB too) for whatever wont fit in the case.
Additional power supply cost is needed regardless. Internal or external drives consume the same amount of power. Again it is not "free" just because it is internal. Lower cost? Sure. Implicit notion that it is free? No.
Whether it is more efficient is Largely depends upon how the data is used. For one-man-shows a fixed amount of data going into a single box works. If multiple people and/or computers need to get at the data putting it all into a single box dedicated to a single user doesn't work so well. Even for one-man-show if the data growth rate is higher than HDD density improvements a single box isn't going to work long term.
Users with not enough money for SAN/NAS typically create "sneaker net" mechanisms for distributing data.
Apple isn't targeting the exact same set of people with the new Mac Pro.
External TB Will NEVER replace internal hard drive bays in the larger market because it will ALWAYS be more expensive as well as less space-efficient, simply due to the need for additional power and peripheral cases. This should be pretty obvious.
It should be pretty obvious that hard drives are being replaced in the larger market. ( presuming you mean larger as in broadly scoped, as opposed to the bigger and heavier case. ).
SSDs don't necessarily need SATA or legacy form factors ( 2.5" or 3.5" drive boxes )
And yes, I will say that Apple "needlessly moved" high throughput expansion and storage outside of the case, unless you're saying that it was "needed" to have the form-factor be this ridiculous bucket, with an army of ugly boxes on your desk holding everything from your platter drives to your sound card.
An army of external boxes isn't necessary. ( Army imply something larger than a very small squad that takes up no more volume than before. )
There is a spectrum of bulk storage solutions that users employ.
But yes this design is not maximized to provision legacy hardware.
There is no reason driven by new Mac Pro design why you diagram has to contain so many boxes.
Mac Pro ---> TB Display ---> Firwire Device.
|||--------> Bulk/legacy storage box with DVD and JBOD drive bays.
Actually is a net increase in available USB ports. ( all USB 3.0 if TB display updates). One additional power cord.
There is nothing about the new Mac Pro that prohibits relatively not well thought out configurations.
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That's a nice idea, but it won't happen. The sort of people who buy Mac Pros are also the sort of people who'd pay $100s on a Thunderbolt accessory. The accessory makers know that, and they aren't going to lower their prices just to appeal to that crowd. Remember, every other Apple computer has Thunderbolt.
The last part doesn't have much impact on the first. If most Thunderbolt buyers are
not money-is-no-object Mac Pro owners why would the TB vendors price their goods to the much smaller group. Wouldn't they want to price the goods so that a somewhat larger target group would buy them?
They don't have to grab all TB capable owners just a larger set.
If there is a motive for companies to make Thunderbolt accessories cheaper, it is to sell to the elusive market of first-year university students who just want an external drive for their 11-inch Macbook Airs because Parallels takes up too much space,
If performance isn't a huge issue that is more inexpensively done with a USB 3.0 drive which the 11 MBA has too. Anyone is who is deeply strapped for money is going to choose the "fast enough" option.
People who download movies because their university proxy blocks streaming, that's who.
People looking to store a limited movie library are gong to slap them onto a inexpensive single HDD that they'll fit onto. Again USB 3.0 can stream that back just fine.
Once you tap that market, you're in the money.
If you can tap that market with Thunderbolt. Basically aiming at the USB heartland. Good luck, probably not going to get a whole lot of traction.