Problem Description:
Since AI team had Y-axis flipped, users who want to keep it the old way have to manually set flags in prefs file to undo these changes:
/isRulerIn4thQuad 0
/isRulerOriginTopLeft 0

It works fine except it breaks setting negative distance in Move dialogue.

Steps to Reproduce:
1. Change said flags to 1
2. Relaunch AI
3. Create and select an object
4. Press Enter to invoke Move dialogue
5. Set vertical position to any positive number and apply
6. Invoke dialogue again
7. Set same vertical value, but negative (you can also select any other object before that) and apply

Actual Result:
Object will move up

Expected Result:
Object should move down

It doesn't matter where you first move object, it matters only that value is the same but has different sign.
It is very annoying bug, because it happens always but in certain cases. Lots of swears and undos.
The way coordinates is swapped via prefs is fine, as long as it just works, although some other vector programs allow to change it via UI.

Any Workarounds:
Set angle manually in dialogue window to desired.
Set bigger position then you need and then move it again to get where you want it.

Attached gif shows almost same situation, but with twist:
I move one object down (with negative distance) and then I want to move second object down and sideways. And when I set horizontal value, AI flips the vertical axis inside dialogue and it force me to dance with workarounds described above.

Adobe denied to admit is as a bug.
Please, help me to prove my point.

I don't ask you to change default ruler origin to bottom left, Adobe already had given us an opportunity to change this by editing flags! I ask for fixing a bug for Move dialogue that is set upon existing and approved behaviour.

I know quite a lot of highly valuable people from Adobe forums who still votes for y-axis go up:
CarlosCanto (he even wrote a script to undo your unexpected making, https://forums.adobe.com/message/3859338)
JETalmage (you should have seen this post back in 2009! https://forums.adobe.com/thread/497089)
Jacob Bugge and all other people who agree with them in comments.

Nobody among my colleagues I know personally likes this. And only two of them having spoken about it at forums. Imagine how many just cry silently.

InDesign is a publishing software, it works with a flow. I don't know anybody who reads from bottom to up (RTL — yes). When you move an object there, you don't move it up, you move it backwards

Photoshop is raster graphics editor, it works with a readable grid of pixels, which are written from top left (we see it every time when images load slow in browsers). Using Photoshop since version 5 I never experienced any trouble with axis going down, because it just never mattered! I retouch photos mostly. People, who uses it for drawing web-design (!) are still OK, because web pages go down. Anyway, PS even hasn't precise move dialogue controls.
And of course, the fact y-axises go one direction, is just a coincidence (when there is only two variants for y-axis to go — it's highly occasional) — because these two programs care for different fields.

But Illustrator is about vectors.
Y-axis goes up in Cartesian coordinate system.
We move objects up meaning up here.
It was a consistency for the sake of consistency.
It was convenient for devs and not end users.
It was a mistake to do.
Adobe should have asked users to vote about denying common sense.
And Adobe should never ever ever had not given users ability to flip it.
And since there is such an ability and I can flip it in Prefs file — I will fight for an ability to work fully.
The worse thing you can do now — is to kill this opportunity.