Regarding Gregg’s Paradox (and thanks for pointing that out: I didn’t know it had a name), the reason we keep all the levels in is that while a taxon may have only one extant species (or whatever), it is possible that there are many taxa that are simply extinct. Given the messiness of fossil taxonomies, we are currently filtering fossil taxa out. However, the goal is to ultimately have everything in there, so (most) problems that involve preserving the taxonomic hierarchy should go away.
Here is how the monotypy issue is represented in Euler/X. Different ranks – same referential extension. Ranks are serviceable for some things (human learning, for instance, though also human erring in “learning”), less so in other contexts. In some contexts asserting that all elements in a monotypic lineage are “the same” is probably acceptable.