Now you know of a case. It was 2000THB (or maybe 1900THB - some things are 1900, some are 2000). Anyway, the school prepared all paperwork with MoE and Immigration and met a group of students at Immigration for the initial visa application. For extensions, they prepared all the paperwork and students would go by themselves to Immigration.
When you're a legitimate student who is legitimately studying at a legitimate school, there are no extras. Lots of pages of documents, but everything is on the up and up. In all the time we've been in Thailand, we have NEVER paid (nor been asked or expected to pay) any "extras". With the exception of what the school handled for the ED Visa, we've always dealt with Immigration on our own and we have never used an agent for anything.
And maybe that's the difference. Things cost more through an agent because you're paying for their time, knowledge, employees, and overhead... not because the agent has to cover "extras" on a your behalf.