I'm not sure of following you, let me bring some insights about the topics you've described.
As you've found sometimes websites can show thousands of elements that can be clicked.
You always are interested in one but the extension needs to show you a number close to all the elements so you can pick the right one. You can make the extension display less numbers describing more context when telling the command. i.e. "click button" instead of "click". In this case the extension will show numbers only next to the buttons.
The size and color of the numbers were complex to choose.
- The size of the numbers is the same than the regular text size of the website, if the user can read the website, he will also able to read the numbers.
- The background color is light yellow (almost white) and the numbers are black. I can show the numbers in bold, but I'm not sure if it will improve the readability.
I think the readability the number will be improved a lot after using the zoom in and zoom out commands. The user will be able to adjust the perfect size ratio where everything becomes clear.
Hope I've answered some question ?