My transport has "tuning dots" what are these?

Likely they are Marigo dots.

Colors include black, green and white. There are several diameters depending on what the "tuner guy" intended.

I have used them and they are definitely audible.

Based on my experience with the Marigo dots I would not put them on Eidolon's. The Eidolon is already a VERY well controlled speaker.

I got positive results with the very large black Marigo's on Fosgate sub woofers (14" driver), but poor results on my Sound Lab speakers except on the back plate. Best was right above the speaker posts, using a green or black was audible, and depending on who was listening the gain was debatable.

I agree with your experience with Marigo on the windows. Large glass windows behave almost like planar speakers when they are bombarded with sound, the Marigo's definitely help dampen that.

If you must try dots, put green Marigo on the back side, upper corner of any piece of audio gear that has rack mount or face plate that extends beyond the chassis. That's a harmless tweak and sometimes helps.