These method books are certainly filled with eye-candy.
Where items are labeled in print, as you described in the first part of your question, I usually add a TN and say something to the effect of "the following items are labeled on the staff:" and then just list each one. I don't believe we are necessarily required to describe the way things actually look. It wouldn't be wrong to do it, but it's not required, in my opinion.
For the highlighted material, I think it would be a good idea to let the reader know what is being highlighted if it's not labeled. A TN is an easy way to take care of that. Or you could come up with a way to have the highlighted element (time signature, staccato note, etc) listed before the music. Just off the top of my head, in looking at the page you attached, the first piece has the whole note and whole rest highlighted along with the time signature. These could be listed after the piece title. If you decide to retain the color on the boxes, you could assign a transcriber created typeform to each color and color code the listed things, too. But the necessity of that could be debated!
Don't you just LOVE method books!!
I hope that helps a little. Let me know if you need more clarification.