Expansion chassis have been part of our landscape for about 10 years or so. It's not about the lanes, it's about fitting that many cards in the system with our I/O counts. I'm in the audio dept, not the picture dept and deal primarily with music. A typical large scale Pro Tools HD system I use is based on a octo Mac Pro though some of the Nuendo rigs are i7 950s and they're plenty big. There is more than just drives with interfacing with Thunderbolt though we use drives like we used tape in the olden days. It's about portability of interfaces in being able to interface different devices, in our apps particularly MADI and fibre channel. You're thinking drives only but there are more advantages to Thunderbolt than connecting drives. An example would be Hammerfall cards in a Thunderbolt enclosure, some sort of drive array and a Mac Book Pro. Fits in a Pelican case and will be dumped to the SAN via fibre channel when we get back so the guys that mix it or put it to picture can have it or we mount it in one of our rooms if we are finishing it. Much of our content capture happens remotely and until recently we'd have rigs racked up and ready to ship out (or send a mobile) but using Thunderbolt as a means to interface what are normally PCIe devices we can have the same capability for many apps in a much smaller foot print and logistically be able to support it better. We still need a truck for live to air but for many things a good flyaway rig that is compact and gets clean tracks is all we need. For the studio rigs we'd need a card to interface the Magma chassis so we might as well use TB. We've been implementing it as needed over the last year and it's been handy (though not cheap).
We could make a Pro Tools or Nuendo system out of the Quo board and have it deliver pro results. But we don't because of several reasons I'm not going to delve into right now but our main obstacle isn't the resource capability of the board so much as no hot swap TB is a deal breaker. Part of it is the support (that we wouldn't get) from using non approved hardware and the grief from Avid for using it. For us the octo Mac Pros and nice MPBs are some of the least costly items.
I think we might be talking past each other, or about different things.
Audio guys have it the easiest as PT, CuBase and Logic consistently needing less PCI-e, less RAM, and less CPU than video guys. If anyone could get by on a Haswell or IB i7-Quad Core then it is you guys, but I don't really see you making that argument here.
You indicate that there is some sort of problem with fitting that many cards in an audio build and maintaining "your I/O count." But you can fit that many in. Just plug them in. Your latency won't suffer because you have a full house and IRQ issues are so 2006. You will not have lower performance in any way. If you want a Fibre card, a 10GbE card, a PT Native card, a quad-monitor GPU, and any other PCI-e card you just plug them in internally simultaneously. Instead of spending that 1K+ on a Magma chassis you can now put it towards a computer that is not obsolete.
Your next example is about using a (granted oldy but goody) 9 year old PCI RME Hammerfall card along with a MBP. How is that relevant? We are talking about towers here, not MBP's reliance upon TB. I completely grant that TB is aimed at MBP, iMac, and Mac Mini users as they have no internal options. Your example is off target and completely irrelevant to any discussion about a tower's motherboard as you can choose to have PCI-e slots.
What could make sense as an advantage is that the modular nature of TB allows you to have fewer fully "built up" computers as you just connect TB devices to whatever you need. That might be a valid argument, but I would challenge you to run the numbers. It might take less organization on the part of your IT guy, but it probably costs you considerably more money in the final tally. TB chassis and Magma chassis are not cheap. Plus, having a tower with a bunch of cables running off it is not exactly a streamlined workstation.
When you do start addressing towers, and studio rigs, you say that you still "need a card to interface the Magma chassis so we might as well use TB." What? Why can't you just plug whatever you have in that Magma into the PCI-e lane directly? Am I missing something here or are you?
You end by saying that no hot swap TB is a deal breaker for a workstation, but you have not yet shown why TB is even needed in an audio workstation. There is exactly one audio interface that uses TB and it also support USB 3.0 as both supply many times the bandwidth it needs.
Oddly enough there is not hot swap TB (or any TB) on either of the two workstations towers that you say that you do use routinely.