I don't think that anyone would dispute that the sentence
I've had enough, thank you.
in reply to a host's asking if the guest would like some more chocolate-covered potato chips, does not constitute a run-on sentence. We're accustomed to hearing people attach "thank you" to a refusal of this sort as an appended signal of politeness, so we don't demand that the construction make sense as single entity when rendered in sentence-diagram form.
I understand perfectly, thank you.
has a lot in common with "I've had enough, thank you." So it seems to me that the crucial question from a reader's perspective is whether we are to read the "understand perfectly" sentence with the same continuous intonation as the "had enough" sentence, or if contrarily we are to read it as a truncated version of two separate sentence wrongly bound by a comma:
I understand perfectly, thank you [for your help/concern/interest].
In the latter case, of course, a stronger punctuation mark would convey the intended sense of the sentence successfully, where the comma does not. Either
I understand perfectly; thank you [for your help/concern/interest].
I understand perfectly. Thank you [for your help/concern/interest].
would do the job. But the writer knows which sense of the original wording was intended; and in the absence of a spoken version of the statement (where hearers could evaluate the statement's intonation for themselves), it seems to me reasonable to suppose that the writer intended the phrase to be understood in the same fashion as "I've had enough, thank you," and punctuated the sentence appropriately to convey that sense.