Hi Laurie. Your question certainly makes me pause. This has been a topic of debate for a long time. Here is my advice. The Nemeth Code tells us to disregard typeform if it is not mathematically significant. Section 34.b: "When any material, mathematical or literary, is printed in non-regular type that has no mathematical significance, the variant type form must not be represented in the transcription."
I would not underline "top 3%" in the braille transcription. If you feel the student will be missing a hint that the print readers get from the underlining, you can inform the reader by means of a transcriber's note that "top 3%" is underlined in print.
Hope this helps.