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I am not sure that I completely understand, it would be a little easier if you described the problem you are trying to solve or what the motivation is.
However, I think that some of what you want to do can be accomplished by inferring gene/protein trees for each gene/protein of interest across different species (including paralogs, maybe?). This will allow ...
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Generally most organisms have multiple copies of the genes/regions coding for ribosomal RNA (since it's needed quite a lot). Additionally these regions can be repetitive or otherwise similar to sequence or place correctly in the genome, therefore it's generally harder to find good genomic sequences for rRNA compared to other genes.
Based on your link, it ...
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23andme uses DNA microarrays ("chips") to perform genotyping. These methods only assay a set of previously known single nucleotide variants, so the probability of missing some specific variant (false negative) is high if that variant is not specifically assayed. It is not quite 100% as frequently known variants missing from the chip are closely associated ...
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