The only part of that I can disagree with is "filing online is quite easy". I've never been able to get it to work in 3 years, but it's not really a problem for me anyway, I'm 20 minutes from my local Immigration office. :)
I believe the "90 day" report can be made up to 14 days before the 90 and up to 7 days after the 90, so theoretically you could stay in the country up to 97 days without penalty.
The question was a simple one - pay for your visa and don't get it. There is absolutely no reason for anybody to assume he was referring to an agent. You appear to be the one on a very shaky soapbox.
I saw no mention of an agent. My interpretation of the question was if you pay a visa fee to the relevant authorities, is it refunded if the visa is refused? The answer would be a simple NO!