Thank you for the question.
First, for now our Guidance does not provide explicit direction for letters that represent blood types or genetic traits.
You are right that the As, Bs, & Os of blood type and the lowercase and capital letters of Punnet squares (which represent combinations of alleles to make genotypes) are not variables. They aren't abbreviations either. They aren't even points on a graph. What are they? The letters that make up a blood type's or a genotype's "name" stand for discrete antigens or alleles. Antigens and alleles are chemical "bits" that are part of, respectively, a blood cell or a string of DNA. So, the letters we're talking about here are similar to chemical symbols for elements (e.g., O for Oxygen, H for Hydrogen, etc.).
Do you have to transcribe the letters of blood types or genotypes within Nemeth switch indicators? I would say no. Mathematical operation is not denoted by the combination of letters representing a blood type or genotype, and the combination of letters will be easily read in either code.
Could you transcribe blood types and genotypes within Nemeth switch indicators? Yes, you could make an argument for transcribing any letter that represents an antigen or allele within switch indicators. But I would not make that argument.
In order to make blood types and genotypes readable, the letters of which they are made up should be individually capitalized in UEB and in Nemeth Code.
Last, because of a technicality, I believe part of your last example must be transcribed in Nemeth Code. Because the key includes equals signs, the letters and words that are connected/compared by those equals signs must be transcribed within Nemeth switch indicators, as part of an equation.
Rock on, and braille on!