So I noticed my polar scope was a little out of alignment with RA axis, i.e. when rotating RA something placed in the center initially wobbles around the center in an ellipse.
This occasionally happens and can be fixed as per the pdf attached above.
After doing this I redid another "mod" I have done to make my polar alignment (PA) even better, I hope.
Firstly, most people perform PA with this type of mount by aligning Polaris to a position on the reticle as given by a polar finder app. This type of PA has some inherent issues, namely parallax seen between Polaris and the reticle when moving your eye around in front of the scope, and also how "level" your reticle is.
The second issue of the reticle is that if your reticle is off by an angle from being truly at the "12 o'clock position" with respect to the horizon/sky, then when you place Polaris in the "right" position on the reticle it will actually be off by that angle that your reticle is rotated from the correct position.
The manual and many tutorials online state that since the Skyguider Pro has a hole to allow the red LED light to illuminate the reticle close to this "12 o'clock position" that you just have to turn RA until the light shines in and you are good to go for PA. I found that the window when turning that lets the LED illuminate the reticle is not infinitesimal, and there is a lot of room allowing the light to shine in when the reticle is far off from being level.
Here is my solution:
First always level the Skyguider Pro or tripod. The tripod being as level as possible provides a consistent reference for each time you adjust the RA to get the reticle in the right position. If the tripod is not level, then the reticle can be off by how much the tripod is tilted.

I use this level I bought on Aliexpress, but I'm sure any level can work.
After leveling the tripod, I then use a distant object that is known to be vertical, like vertical edges on a building, or a radio tower / mast.
I then adjust the RA such that the reticle's vertical line is aligned with the vertical edge I am referencing.
Here you can see when I move the altitude knob of the Skyguider the tower in the view stays along the vertical line of the reticle:


Now that I know the reticle is truly "level", in the "12 o'clock position", whatever you wanna call it, to the best of my ability, I mark two reference points as shown below with a silver sharpie:

One mark goes on the red stationary part of the Skyguider, and the other mark goes on the polar scope, so that they are aligned.
Now in the field, when I level my tripod, I just moved the markings together and I know my reticle is as good as it can get. Then I perform PA.
I hope that someone finds this useful.