As far as end users are concerned, I would agree thin Mini-ITX is mostly irrelevant, and I wouldn't be surprised if that also happened with mSTX as well, but I don't think either is obsolete or irrelevant on the whole. There are still plenty of newer AIOs that use Thin Mini-ITX even if it isn't a majority (as you mentioned proprietary means you can get an optimal layout, it's the same reason there's no such thing as a standard laptop form factor)
The whole point of both was to standardize certain form factors that are already in use. For Thin Mini-ITX this is All-in-One PCs, and for mSTX this is mini PCs. Previously they were proprietary which meant each manufacturer had to do their own engineering work separately and often parts wouldn't even be interchangeable between models, but by standardizing main components, it becomes much easier for system integrators to build a complete system with fewer expenses. The problem is those are also somewhat niche markets and the overall PC market is already contracting with the proliferation of more powerful mobile systems (phones and tablets), better apps for them, and the fact that many people only ever had PCs to begin with for internet, video and casual games which mobile devices did fairly well almost from the outset. The small market for AIOs means that most of the stuff is available only to OEMs, and I suspect the same might hold true for mSTX.
Another thing that is noteworthy for both is that people who build their own PCs tend to do so because they are trying to chase a certain price-performance point for their PC which is more relevant as the system's power increases and higher priced components become involved since pre-built machines carry a price markup. You can easily get a system that can browse the internet for a couple hundred bucks, and the extra you pay going pre-built can be paid from what cash you have in your wallet, but high end machines often cost a few hundred dollars more than what it would cost to build it yourself which makes researching, buying and assembling the components more worth the time.
Given that, I do think that a lack of motherboards and enclosures that support discrete graphics is detrimental. You can get decent CPUs and good storage and memory capacities, but by not having any real graphical horsepower, I think it shuts out a sizable portion of the people actually interested in building their own system. I think it would also shut out OEMs that want to offer one of those form factors boasting their gaming power. While I have seen Thin Mini-ITX motherboards and enclosures that support MXM modules, there are only a few of those; most manufacturers still go completely custom where that is concerned.
Of course there's also the big catch-22 issue, people (including system integrators) aren't buying because there isn't much on offer, and there isn't much on offer because not many are buying.
We have seen this sort of thing before in the user space. MXM came about to ease manufacturing costs by standardizing GPUs for small systems (mainly laptops), and now, laptop manufacturers use them heavily to make it easier and cheaper to build a system, but while they tend to tout the upgradability of the GPU, it's hard for the end user to acquire an MXM module, and there is a significant price premium for doing so. (SO-DIMM, mPCIe, and M.2 exist for a similar reason, letting system integrators complete their systems using off-the-shelf modular parts, though those are easily acquired by end users)