Thank you for this interesting question. In physics in particular, there are many constants that use normal (unitalicized) lowercase Roman letters. In the print copy they are distinguishable from variables because the variables are in italics. In braille, the italics are disregarded. Within the context of the subject matter, it should be clear to the reader whether the letter represents a variable or a constant. There is no need for the transcriber to explain.
However, if the two identical letters are used in the same equation or mathematical statement, we may have a clarity issue. I quickly found an example involving the electrostatic constant which shows a normal lowercase letter e and an italicized lowercase letter e in the same expression. In that case, the normal "e" is part of a larger unit "eV" (electronvolt) so I expect the second e, which is a variable, will not be confusing.
The topic of identical letters in two different typefaces in the same expression is under discussion in the BANA technical committees. As the rules currently stand, the distinction between normal and italics is not shown in the braille transcription.
If you would like to attach some examples of what you are finding in your work, we can discuss this further.