I like this kind of debate, logical founded on evidence than speculation an personal saga. Thanks for give this thread a bit of good taste.
Now, fight ¡
<grin>
What you accounts it's true and fair, I'm paying an extra 1000$ for what could cost much less on a cMP at same performance, I assumed this cost for the same reasons, on the nMP you don't have options for a 2nd internal ssd (which would replace the little big disk at a competitive cost also paying Apple 's tax and save about 400$ and have a more solid system.
But the external 2big (I've the 6TB Version) is meant for continuous time machine, also having the choice to have those two spinners inside the Mac our choice is to use it externally, since in the event my nMP passes away on is stolen (that's why I store this on a safe) I'll restart my work in just minutes from where I left ASAP I got an replacement workstation.
Well....to play a little Devil's Advocate off the bat - - if your desktop machine were a bit bigger/chunkier, perhaps you wouldn't have to worry as much about it being stolen <g>.
But actually a bit more seriously, from a security standpoint, the cMP (and its internal contents) are more readily secured than a lightweight nMP, particularly when we then have to include each external component as well. The difference (and nuance) is when we go to very high levels of security where we're talking about literally locking up the data every night in a literal safe ... and in this regards, I know that my local IT would rule that the internal SSD blade of the nMP would have be included in this too, which means a safe drawer to drop the whole thing in each night in addition to external drives. In contrast, the old cMP's four 3.5" tray design would be just as quick & easy ... and take up less room in the safe.
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Moving on, for putting an SSD into a cMP, there's IMO pragmatically 3.5 options. The first is a 2.5" adaptor to use it on one of the 3.5" trays .. but this is a poor choice because its interface is only SATA-2. The second would be to use the spare optical bay (or both), but same SATA-2 limitation. The third is via PCIe card(s), where the payoff is performance. I'm currently using one OWC Accelsior (dual blades), but I also picked up in 2015 the much cheaper/flexible Accelsior "S" card, which is basically just a single port SATA-3 onto which one mounts a single 2.5" onto (HDD or SSD). And Sonnet makes a similar style card, as well as a long card which can mount a pair of 2.5" drives. I've also seen an mSATA PCIe adaptor board being sold now too...OWC, if memory serves.
Finally, the remaining "0.5" is something I can recall seeing once awhile back - - it was an adaptor bracket from which one could hang four 2.5" drives off of internally, which would then be paired with a PCIe SATA card to provide the four interface ports. Can't recall who made/sold it.
In any case, what I can easily envision as quite feasible in the design of a notional future cMP would be not only SATA-3, but other modernizations as well, and I think it is quite reasonable to get a space claim on the motherboard for having some SSD blades, primarily for the boot drive. Bonus points here would be to double this up so that one could have a {boot + mirror of boot} configuration ... see comments on the rationale for having a boot mirror by Digital Lloyd (MacPerformanceGuide).
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Next, onto Time Machine.
My current cMP configuration is two of my 3.5" bays occupied by a pair of HDDs in RAID0 (2 * 2TB = 4TB), as my primary work space...they're turning at ~230MB/sec, which is okay (my benchmarking on the Accesior "S" PCIe card is ~500MB/sec). Given that these drives are now 3 years old, they'll need to be retired soon (reliability), which with the declining prices of SSDs may be changed over ... I'm not sure right now if I'd RAID0 the SSDs or not for the performance boost or not (I'm not doing 4K yet to really benefit)...
Bays #3 and #4 each have their own 6TB drive, with each one allocated separately into TM for backups. OS X automatically alternates between the two 6TB drives.
Finally, I use externals for my off-site backups. These are currently a few remaining USB externals but primarily a bunch of bare internal hard drives (a few of which were pulled from service early, due to being "small" capacity): rather than installing these into new cases, I use a "Drive Dock" (see:
http://eshop.macsales.com/shop/NewerTech/Voyager/Hard_Drive_Dock ). While cost started as the motivation, the real benefit came from organizational streamlining: it sidesteps the hassle, mess & time of needing to keep track of a dozen different brand power supplies, since the power plugs on external hard drives aren't standardized.
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Hope this helps reveal some of the rationale of my current setup, and what its eventual replacement implications are going to be.