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<If you watch a species split very closely, generation by generation, over
time, there will generally not be any particular point where you can say
that a new species (let alone higher taxon) has emerged.>

Kind of like an occasional visitor notices changes in kids faster than
parents do.
I would make a comment about how the change is significant when the
descendant can be defined as a new species, but I remember a good posting on
the list awhile ago about how speciation is a confused and confusing subject
these days.
However, making the assumption that there is a useful definition of a
species, you are implicitly agreeing that an observer or generations of
observers would be able to observe and identify the (slow) inception of a
new species, even if the exact point of divergence remained in dispute.  As
new species continued to arise, the observers would be able to identify a
related group.
Your original observation:
<At some point or another, every honest taxonomist must admit to him- or
herself that if we truly had the capability to observe the origin and
development of every individual organism that ever lived on earth, we would
find that there are no distinct groups to name.>
The appearance of a species (and group of species) could be observed, but
your question seems more definitional, about when lines are drawn.  Because
the animals are unaffected by the decision and the issues involve naming and
defining, you're talking about an inference.
I'd explicitly extend your concern with inference (as I'm reading it) to the
question of how inference is used in place of observation to create
taxonomy.  Whether limited data make it easier or harder to identify a split
in a lineage, the absence of a sufficiently complete set of observations
means the taxonomist must draw conclusions based on principles.
I would be appreciative if you said that classification remains a
well-educated, arbitrary (in the sense of creating rules beyond the data)
inference, but I'm not sure that's what you intend.
Thanks for taking the time to explain.