Consider a system that had 6mm diameter "blanks" and a tool that would let you put down an epitaxial layer, lay down, expose, and then etch a resist layer, etc. At those small scales, one could hope the chemistry would be manageable.
It's really hard to see what benefit there might be to trying to cram all of this into a shipping container, other than to say you did it.
I am envisioning a handle which ends in stainless steel holding mechanism that has the feature that when you slide it into a 'production' slot the holding mechanism pushes back to reveal the sample's surface. Think window on a floppy disk only better at keeping dust out.
6mm is pretty small (about 1/4" to be precise) in diameter. Call it 25 mm^2 of area, you're looking at, maybe, 10K "device elements" you could lay down (I'm guessing you lose a bunch of space to 3 - 8 "pads")
Your "fab" is a machine that sits on a desk, it has tanks that hold 'consumables' that are used in the process and a tank that fills with waste output. Both the empty consumables tanks and the full waste tank are shipped off to be disposed of properly.
On working side of the fab there are ports that are of the same shape as the end of your sample holder. They positively lock so you push the sample holder into the port until it "clicks" and then the machine does an evacuation cycle, followed by that step of the process.
Building a device would consist of loading your design in, then using the various ports (sometimes more than once) for different steps (add resist/render layer mask) (cure resist/rinse uncured resist off) (etch) (dope-p), (dope-n), (metal), (poly), (package).
The 'package' would always be the same shape. Think a metal can transistor from the 80's. With 8 leads and a pin 1 tab. What leads were connected would be defined by what you had programmed for your device.
You do all the steps (it would probably take anywhere from 1 to 3 days depending on the process steps you used). And the result is this part you made. Plug it into your characterization harness and verify it's function and/or signal parameters. If it fails you toss it and do another one, if it passes you have your bespoke device to use in your project.
I certainly don't see something like that having mass market appeal but I know you could sell them.
If you looked into some of the early cheap Chinese glow-pattern trinkets and musical greeting cards, the IC often looked quite "home made", having a central irregular blob of epoxy covering the fabricated device in the middle of a small square ceramic substrate. With a few not-so-thin wires coming out from under the epoxy, tieing it into the discrete components, if any.
I would imagine at the time the primary requirement was for the component to simply cost less and be way smaller than an alternative stuffed PCB, without any real need for it to be fabricated as one of the actual "chips" off of a silicon wafer.
Depending on what power of "microscope" you are willing to limit yourself to, it might not be as difficult to see microchips (or at least micro IC's) in your forseeable future.
That said, there are people on youtube that are doing it, and it's doable to some degree in a garage environment, but the risks of dealing with hot HF acid are too much for most of us.