Thkx a lot @blh64 it worked!
I'm amazed, a little pissed and very happy at the same time 
I'm amazed by the simplicity of the fix but a little pissed since I knew we needed to have common ground reference.
Still learning and I thought the ground wire from the power supply to the driver was enough and didn't needed to also provide the same ground to the Arduino.
And I was under the impression the driver was handling everything regarding current control to the motor and the Arduino handling the logic call of the direction and step sequence without needing a ground common reference.
But it turn out @blh64 was right and providing the common ground reference to the Arduino from the TMC2209 driver is essential!
The "fixed" schematics:
Here you can see the "brown" wire which spawn from the wire "bridge" between the GND and EN pins on the TMC2209 and is then connected to the GND pin of the Arduino:
The back view showing the wire connection linking the TMC2209 GND and EN pins to the Ardhuino GND pin:
I knew I was missing something fundamental in my setup for negative speeds to fail completely like that.
Here is the fix in action:
Hoping the detailed rundown we went over will help the next person hitting a similar issue!
Thkx again @blh64, I'll be able to push the project forward now!
@JCA34F That project started a year ago and I was gathering some components without exactly knowing which type of motors and how many I would end up using.
Turn out the power supply I got back then was overkill for the very small motors I'm glad I found on Stepperonline.
But yeah, it could have gone down in many different ways.
@groundFungus The schematic was a bit misleading about where the pins from the driver were actually connected to.
I provided the details in the post above the picture showing the connection between the TMC2209 and the Arduino (TMC2209 Dir pin in the Arduino pin 2 / TMC2209 Step in in the Arduino pin ~3).
But yeah, every details count so thkx for checking!
@sof_7 I hope you marking your board with a sharpie work your way, whatever you are trying to achieve.
I'm glad I asked for help on this forum, have a good day everyone! 