"...large case, at which point we have to ask whether the MSI AIO even makes sense."
I picked a mid-tower which can mount i.e. 240mm AIO at the top, and 280mm or 360mm AIO at the front. And yeah, the shorter length wouldn't be much a selling point for me.
On the other hand though, in my case I have e.g. a Gen4 M.2 slot with heatsink at the bottom of the MB, which would be just below the intake fan/s of a four-slot GPU. And if that heatsink in operation, e.g. with a 990 PRO, would have an impact on the cooling of the GPU, then GPU AIO could make sense.
And one step further, a Gen5 M.2 SSD will apparently need some active cooling. And an air cooled (model of) 4090 dissipating heat into the tower, that may not be all great (and bottom mounted intake fans may not help much to cool that SSD above the GPU).
That is a bit speculative at this point of course. Albeit to my defense, a lot of the talk on the internet about these issues turn around stuff such as whether to mount the PSU with the intake-fan upwards (which I don't find to be the best idea). But just meant to expand on the question, with there possibly being some practical arguments for a 4090 AIO solution even with a bit larger mid-tower - if AIO is something an user finds to be acceptable.