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The cost of drive bays is added space, that is obviously correct - power requirements are lowish, the extra engineering and design effort for drive bays is indeed trivial , so are hardware costs .
It's a complete redesign after all, so that's small potatoes .
In the past though, Apple has done Apple labeled drives to go with their systems. Certifying drives costs money and so does long term contracts to buy specific models There is a bit more costs here than you are pointing out. I agree it isn't a huge cost, just higher than you are making it out to be.
There is also the problem if the the Mac Pro is the last Apple device using a 3.5" drive. If there is a "buy/certify 3.5 drive " spot in the personnel line it sticks out much more than when Airports , iMacs , Mac Pro , and XRaid were using them. ( and iPods , laptops , and mini used smaller ones. )
If the mainstream iMac gets revised to drop the 3.5" drive ( for more cooling) then Mac Pro is going to be out there on a limb. If all Apple is still buying in bulk is 2.5" drives then those may be what they go with because it is cheaper (costs less), because there is volume and work to spread costs over more systems sold. 3.5" drives are
not likely at all going to be part of the standard configuration. So this is BTO drives for folks who may / may not buy them. They fewer 3.5" drives Apple sells the higher the price goes until get to negative feedback loop because most of the buyers are off buying "as cheap as possible" stuff off the third party market. There is probably going to have to be some kind of floor of volume for Apple to jump in.
No need to lose other features or increase the price either due to a few added drive slots .
Besides - if Apple use your kind of approach, we will not just lose drive bays, your PCIe slots will be lost too .
It's the kind of attitude that gave us the tcMP .
PCI-e external boxes ( often used for eGPU solutions ) means Apple will probably be dealing with GPU cards whether they are placed in a Mac Pro or not. Not down to the last reminding sole system. The "Computational" GPGPU is a real thing. It didn't work as the entry configuration requirement for the Mac Pro, but it is deployed often enough that Apple will have to keep up with it to some extent. it isn't going to drop down to zero across most of the Mac product line.
That wasn't the baseline requirement though that moved the MP 2013 into the space it went. Apple's drive to do a literal desktop solution. If they are stuck on that then won't see four bays at all. It is only when the footprint constraints are loosen back to older deskside system where "enough volume, no problem" starts to creep back in.
Imagine a cMP like design without the optical bays, smart packaging and cooling, and a case using a more weight efficient structure and materials . No handles either, those must go ...
Hell, make the power supply external, how's that for redundancy ?
Apple is very unlikely to let go of Al-lu-min-um . The whole rest of the is aluminum. Plastic isn't very "Green". So 3.5" bay height probably does make a weight difference. If it is floor standing don't be surprised that some handles are still there ( Apple's symmetry OCD ). If they shrink it some the additional handle height won't be standard rack hostile.
You have left off quieter which is probably coupled to the cooling, which likely will be a constraint. It has been before, nothing indicates they are doing a 180 on that. ( it may not have to limbo down to the MP 2013 levels )
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Apple can make great computers, they just have to find their way back to form and function .
I think it is more about loosening up a bit about letting people put stuff they don't buy from Apple in the box. Apple doesn't want to be just a container builder. However, there is an intersection on just how far back they can retreat on that. Mac Pro has to integrate in with other stuff that folks bought that may cost more than the Mac Pro itself. Apple can't turn it into a "tag wags dog" context.
However, the opposite is also true, highly inexpensive 3.5" drives being the primary driver of a system requirement is a "tag wags dog" context.