That's fair. From what I hear, thunderbolt GPUs are a fair bit more finicky than internal PCIe ones, so for a desktop I'd still say having an internal GPU is better, but it should at least be a reasonably good workaround.
It's a bit sad to trade reliability, GPU performance, tidiness (since the external enclosure adds more boxes and wires and power supplies), price, and CPU power just for a smaller core computer though.
It gets even worse when you want a couple of big HDDs which would have just gone in drive bays with a traditional computer. With the mac mini, you'd have to add even more expensive external enclosures to your desk, which is expensive and messy. Suddenly, instead of a nice self-contained smallish desktop, you have an impressively small core machine box, with a wire to your GPU box (which has to be on top of the desk due to the short length of thunderbolt cables), a wire to your HDD box, and you still have the slower CPU.
I don't really mean to say the Mac mini is a poor choice, it probably fits a bunch of desktop use cases reasonably well. It's just not as optimal as it could be.
To illustrate how a real small and powerful desktop from Apple could've been: I'm using a really small (though not as small as the mac mini) Fractal Design Node 304 [0], with a 2.5 slot width, full length GPU, a 3.5" drive, two 2.5" drives, an m.2, and a standard ITX card with regular RAM and CPU slots. I have a 1080Ti and an i7 6700k in it with no thermal issues. Apple could've made a similarly expandable machine in a smaller form factor with better thermals and looks, but they... don't.
[0]: https://www.fractal-design.com/home/product/cases/node-serie...