What is the point of setting an upper limit in Auto-ISO?

Less DOF than what other option? Less than with a slower lens, AOTBE, but not less DOF than a FF camera and lens giving the same photon noise and image-level diffraction. It's always down to the pupil size, and distance from the subject, for these three parameters for a given subject in given light and a given exposure time.

There's no reason that a camera couldn't have an option to increase the shutter speed beyond that set by the user in M mode, to avoid clipping highlights. That could be useful with both manual ISO and auto-ISO. Canon has already provided an option in some recent cameras that can change shutter speed in M mode when you zoom a zoom or add/remove TCs, so Canon could not claim that the option that I wish for would "go against the spirit of Manual".

If the camera is on a tripod, presumably you have plenty of time. In that situation, what possible advantage does auto ISO offer?

You cannot change shutter speed in auto ISO in my menu on Z9, but you can on Z 7II and Z 6II

Do opinions change if after a certain ISO noise reduction is applied, say 6400?

Some camera manufacturers appear to be applying some form of noise reduction (that isn't user controllable) after a certain ISO. -based on what I saw on that photonstophotons link earlier.

My philosophy of a raw image workflow is to never do anything in camera that can't be done at least as well in postproduction.

According to P2P, some cameras apply mandatory NR at base ISO (Canon R5) or throughout most of the ISO range (Pentax K3 III). The NR in those cameras does not bother me. Before deciding to avoid higher ISO ranges because of NR, you should decide whether it bothers you.

A useful test shot? ;)

Ah, yes. I've been using MILCs too long.

With DSLRs, I would use LiveView for a test shot on a tripod.

That's because you don't use polaroid backs ;)

I just threw away an 8x10 Polaroid processor. Those were the bad old days.

I avoided using polaroids for test shots as much as I could. It was too expensive in USSR :)

8x10 Polaroids were expensive in the States, too. Ten bucks a shot, as I remember from the early 90s.

3x in USSR in 70s-80s, and that is if you are lucky.
I mean, when it comes to test shots with digital cameras, many things may work well. Most of the times when using a tripod I also use a small notebook (Linux or macOS) and the shots go there and into RawDigger. Camera is set to base ISO.

Perhaps they only filter raw levels so close to black that you are not likely to see it in a typical exposure. A real-world, high-DR scene usually has sufficient global flare and nothing in the scene is black enough to record near raw black. When you use the shadows for exposure latitude of a low-DR scene and "under-expose" it grossly, then darker tones do approach raw "black" and you might see the filtering more there.

In my experience with Nikon, Sony, and Fuji cameras, they are not that smart.

My Ricoh GRiii has a custom setting called "One Push AE in M Mode".

It can be assigned to any one of several buttons on the camera and then when in manual mode you press the button and it automatically adjusts either the aperture, the shutter speed, or both (depending on another custom setting).

So then even in manual mode you only need one button to get a proper EV. This makes manual mode so much faster...