Here's the relevant quote from Cho that I'm agreeing with, if only in part:
"I don't know why the Comics Journal gets so bent out of shape about self-nomination, since they do it themselves." He then goes on to recite a refrain I'm sure Fanta people are heartily sick of, that four or five of the top 10 are Fanta books (I'm sure it's right up there with the song about TCJ being nothing but Fanta's house organ). So, although he does say he wishes he had not gone ahead and self-nominated, he does also
criticize you guys, and I find that worthy of discussion (hardly a "reflex").
What are the key differences between Cho's self-nomination and the Top 100? Well, contrary to what you wrote Cho's self-nomination doesn't claim he's one of the greatest cartoonists of all time; just the best in a particular category during the year the Ignatz was awarded.
Another would be that the Top 100 confers no award as such, except having earned the difficult-to-receive approbation of six JOURNAL writers. As I said, I think the end is still the same, though; to champion this or that work of comic art.
And lastly, as you say the Ignatz is voted on by a popular audience rather than by six guys in the industry. But neither process is more or less "legitimate" than the other, any more than the Nebulas are more so than the Hugos. Perhaps if you elucidated what you meant by "sheen of legitimacy..."