What you're talking about doesn't sound correct. You apply for the Work Visa, and then you get 3 month Non-B visa, and once in Thailand apply for your work permit and then your extension of stay. At no point should your work permit hold you up from staying in Thailand.
The non-b Visa can be granted in 1 day if all your paperwork is in order.
but he’s right. All the time waste stuff your friend needs to still be present, at the embassy or online etc. also has to provide the documents to apply.
So the only thing an agent can do is help you organise it, but it’s stupidly easy and straightforward.