"The downside is that you have a ton of programs and other files on your boot drive that you hardly use, hogging up precious fast SSD space, and lots of files and other things on your HDD that COULD be on your SSD if you had room."
Absolutely NOT.
I have no less than seven (SEVEN!) mounted volumes on my desktop at all times.
I know where all my files are, and I manage them carefully.
I keep 2 boot volumes (system, apps, accounts), 2 "main" volumes (the bulk of my day-to-day data), a "Music" volume (obvious), a "Media" volume (pdfs, video, pics), and a "General" volume (odds and ends). Plus I maintain an external backup drive and regularly dupe the contents of each volume to a backup.
"if you do any heavy lifting at all, it's nice to use the SSD much more efficiently than you can manually manage just by moving stuff around at the files/app/package level."
Everything on all my volumes is "managed" well enough and better than the OS could manage them as I wanted, thank you very much…
So you are saying that every program, every cache, every preference, EVERYthing at the BLOCK level on your SSD needs to be there?
I am not commenting on your organization/filing system - it sounds quite neat and tidy. A place for everything and everything in its place. I AM commenting on your ability (or lack there of) to mange the contents of your SSD and HDDs at a level of granularity not possible when managing files/programs/packages/etc.
Case in point - my Aperture Library is 100GB and growing. And that's having it set up as "referenced", which means all of my source images are on an external FW800 drive and take up 400GB of additional space. Inside my Library are all of my videos (I keep them in my Library so iMovie has access to them and can organize them by date), the "versions" of all my processed images, all of the thumbnails and all of the previews. I have video and images going back to 2003. I can NOT break that Library down into any smaller size, even though I only use 5% of it on a regular basis. So in my old manually-managed 240GB internal SSD / 2TB FW800 external HDD arrangement, 42% of my SSD was taken up by my Aperture Library, even though I used no more than 5% of it at a time. That is VERY inefficient, but it is what I had to do to have the user experience (snappy photo editing) that I wanted. It also meant that I was continually pruning things from my SSD, continually moving video in and out of the Library, and going through all sorts of things to manage my precious SSD space.
Enter FD. I have my Aperture Library on my FD array, and when it was first put on it appears to have been put onto the HDD portion of the array. The first time I launched it, it was slow, and I could watch in iStat Menus that the HDD was getting a workout, populating all of the thumbnails and other bits of the database that loads. Ditto when I would work on recent shots. However, after launching it a few times, it began to load much more quickly. I can see by watching iStat Menus that the SSD is now getting a workout, and the HDD is idle. So the portion of the Aperture Library that loads when launching Aperture is now on the SSD, but the rest of it (all of those video files, previews, etc.) that don't load when Aperture launches is still on the HDD. The first time I opened a project to work on the images in it I could see a slight lag. However, as I worked on those images over the next few minutes, it sped up. Now, when I go back to an image I already worked on, it's SSD quick. So I know that those "blocks" of data have been moved to the SSD. So now I have maybe 1GB of my Aperture Library on the SSD while 99GB is still on the HDD.
In place of "Aperture Library" put "Lightroom Library", "iMovie Projects", "FCPX Projects", etc. Now suddenly, you don't have to choose where you put these things and move them around based on what you are actively working on. You put them all on a huge FD array and let OSX figure it out for you.
As my needs and usage change, the location of my data AT THE BLOCK LEVEL changes. You can't manage data at that level manually, and you can't continually optimize your data to the level of optimization that FD does. "Optmization" and "organization" are NOT reasons to not use FD. Being leery of new technology, hesitant to set up an FD array yourself, large file moving or importing, risk-averse to doubling the possible failure rate (although the doubling of a small number is still small, and mitigated with a sound backup strategy) - those are all good possible reasons. Being able to optimize your data and user experience, not so much.
And then there is the segment of the population that just does not like to give up control of anything. They don't like that Aperture stores things in a Library, they don't like the way that iWork stores things in iCloud, they don't like having to use iTunes to interact with their sound files. They want to do EVERYthing from the Finder, and NOTHING via managed apps. I am not one of those, having given up that sort of control when moving my home-based computing off of Windows some years ago. But I understand that some folks are like that, which is why auto manufacturers still make stick shifts, people still want a paper paycheck instead of direct deposit, and non-programmable thermostats still sold.